Document:

<PAGE>

                                                                   EXHIBIT 10.20

                                               Confidential Treatment Requested
                                             Under 17 C.F.R. (S)(S) 200.80(b)(4)
                                                      200.83 and 230.406

                            COLLABORATION AGREEMENT

     This Collaboration Agreement (the "Agreement") entered into as of June 28,
1999 (the "Effective Date"), is by and between Rhone-Poulenc Animal Nutrition
S.A. ("RPAN"), a French corporation with headquarters located at 42 avenue
Aristide Briand, 92160 Antony (France), and Diversa Corporation ("Diversa") a
Delaware corporation with headquarters located at 10665 Sorrento Valley Road,
San Diego, California 92121, collectively the ("Parties").

     Whereas, Diversa has expertise in the discovery and development of, and has
discovered and developed enzymes, as well as proprietary technologies for the
rapid discovery, development and optimization of enzymes;

     Whereas, RPAN has expertise in the use of enzymes and in particular for the
production of [*****].

     Whereas, RPAN and Diversa wish to collaborate to discover and develop a
[*****] to be used in the production of [*****] as set forth in the project plan
attached hereto as Exhibit A (the "Project Plan").

     Now, Therefore, in consideration of the mutual covenants set forth in this
Agreement, the Parties hereby agree as follows:

1.   Definitions

     "Base Catalyst" means the catalyst provided by RPAN to Diversa comprising
the RPAN Enzyme (defined below) immobilized in [*****].

     "Catalyst" means the catalyst comprising an Option Enzyme (defined below)
or a Licensed Enzyme (defined below) immobilized in [*****].

     "Catalyst Activity" means activity obtained in Phase V of the enzyme
performance assessment procedure as set forth in Exhibit B hereto.

     "Derivative Enzyme" means any derivative of the Licensed Enzyme derived
through Diversa's application of the Evolution Technology or any [*****]
discovered through the use of the RPAN Enzyme in the Hybridization Technology.

     "Enzyme" means any [*****] discovered and/or developed by Diversa for RPAN
during the course of the collaboration.

     "[*****]" [*****].

     "[*****]" [*****].

     "Licensed Enzyme" means the Option Enzyme licensed to RPAN upon exercise of
the Option.

     "Option Enzyme" means the Enzyme provided by Diversa to RPAN for evaluation
under the Project Plan.

     "Product" means [*****].

                                      1.      *Confidential Treatment Requested
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     "RPAN Enzyme" means the [*****] provided by RPAN to Diversa under this
Agreement.

2.   Collaboration

     RPAN and Diversa shall collaborate to discover and develop an enzyme having
[*****] activity to be used in the Catalyst to produce the Product as set forth
in the project plan attached hereto as Exhibit A (the "Project Plan").

3.   Option

     3.1  Option Grant.  Subject to the terms and conditions of this Agreement,
Diversa will grant to RPAN an exclusive option (the "Option") to obtain an
exclusive, worldwide, royalty-bearing license (the "License") under Section 4.1
to use one of the Option Enzymes to produce the Catalyst and the Product.

     3.2  Option Period. The Option will commence immediately upon delivery of
the Option Enzymes satisfying the criteria set forth in the Project Plan, and
remain in effect for a period of [*****] thereafter (the "Option Period").

     3.3  Exercise of Option.  RPAN may exercise the Option by providing Diversa
written notice of the exercise of such Option at any time during the Option
Period. If RPAN does not exercise the Option during the Option Period, the
Option shall expire, and RPAN shall have no further rights thereunder and both
parties shall return or destroy all forms of Confidential Information provided
to the other party under this Agreement relating to the discovery and
development of the Option Enzymes subject to such Option, within [*****] after
such expiration.

4.   License Terms

     4.1  License Grant. Upon exercise of the Option, and payment of the license
fee set forth in Section 5.2 herein, Diversa will grant to RPAN an exclusive,
worldwide license, including the right to grant sublicenses, to use the Licensed
Enzyme to the extent necessary to make and have made the Catalyst to use in the
production of the Product (the "License").

     4.2  Term of license. The License will become effective upon payment of the
license fee as set forth in Section 5.2 and will continue, in any country, until
the expiration of the last to expire patent rights covering the Licensed Enzyme
in any country (the "Royalty Term").

     4.3  Right to Sublicense.  RPAN will have the right to grant sublicenses to
affiliates and third parties, provided that the terms of such sublicenses are
consistent with the terms of this Agreement.

     4.4  Right of First Refusal. RPAN will have a right of first refusal to
obtain a license from Diversa to use the Licensed Enzyme to make and have made
certain molecules related to the product specified in Exhibit D ("Related
Molecules"). In the event that Diversa proposes to grant such a license to any
third party. Diversa will notify RPAN in writing of the offer of such license
and the terms upon which such license is proposed to be granted to such third
party (the "Offer"). RPAN shall have a period of ninety (90) days from the date
of such notice in which to review the Offer and notify Diversa in writing that
it wishes to acquire such rights on such or similar terms. If RPAN provides such
notice within such ninety (90) day period, then the parties shall proceed
diligently in good faith to enter into a definitive agreement with regard to
such rights on customary terms for similar licenses. If RPAN does not provide
written notice of its wish to acquire such rights or provides written notice
that it is not interested in acquiring such rights on the terms presented in the
offer within such ninety (90) day period, then Diversa shall be free to grant
such rights to a third party on terms no more favorable to such third party than
the terms set forth in the Offer.

                                      2.      *Confidential Treatment Requested
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5.   Payments

     5.1  Research Funding Payment. Upon execution of the Collaboration
Agreement, RPAN will pay [*****] to Diversa, a payment which is estimated to by
[*****] of the total costs required to conduct the research hereunder. Diversa
will fund the remaining [*****] of such costs.

     5.2  License Fee. Upon RPAN's exercise of the Option as set forth in
Section 3, it will pay Diversa a non-refundable license fee of [*****].

     5.3  Royalties. RPAN will pay Diversa a royalty equal to [*****] of the
cost savings ("Cost Savings") generated by using the Licensed Enzyme in the
Catalyst to make the Product. The Cost Savings will be calculated from the work
performed in Phase V of the Enzyme Performance Assessment Procedure defined in
Exhibit B attached hereto. Further, the [*****]. In the event the Catalyst
demonstrates [*****] and a [*****] over the Base Catalyst, as determined from
the tests performed under Exhibit B, RPAN will pay Diversa a royalty of [*****]
of Product produced by RPAN, its affiliates or sublicensees. Said payment shall
be based on estimated cost savings in the Catalyst of approximately [*****] of
Product produced. RPAN and Diversa will mutually agree upon the applicable
royalty payable to Diversa for [*****]. Such agreed upon royalty shall be in
writing and attached hereto as an addendum. For increases in [*****], the
royalty will be equal to [*****] (See Exhibit C).

     5.4  Royalty Period. Royalties shall be paid on a [*****] basis. Each
[*****] in which the Cost Savings are generated from the use of Licensed Enzymes
in the production of the Product shall be a "Royalty Period". Royalties are
payable within [*****] after the end of each Royalty Period.

     5.5  Reports.  At the same time as each royalty payment is due, RPAN shall
deliver to Diversa a report based upon the Royalty Period for which the payment
is due, containing the following information:

          (a)  Cost Savings generated during the applicable Royalty Period;

          (b)  Calculation of amount due to Diversa.

All amounts payable under this Section will first be calculated in the currency
of sale and then converted into U.S. dollars.  The buying rates involved for the
currency of the United States into which the currencies involved are being
exchanged shall be the one quoted by The Wall Street Journal at the close of
                                     -----------------------
business on the last business day of the applicable Royalty Period. Such amounts
shall be paid without deduction, except as required by law, of any withholding
taxes, value-added taxes, or other charges applicable to such payments

     5.6  Records. RPAN shall maintain complete and accurate records of the
Licensed Enzyme used or sold by them or their Sublicensees under this Agreement,
and any amounts payable to Diversa in relation such use or sale, which records
shall contain sufficient information for Diversa to confirm the accuracy of such
records. RPAN shall retain such records for at least [*****] after the
conclusion of the Royalty Term. Diversa (acting as the "Auditing Party") shall
have the right, at its own expense, to cause an independent certified public

                                      3.      *Confidential Treatment Requested
<PAGE>

accountant reasonably acceptable to RPAN, to inspect such records of RPAN (the
"Audited Party") during normal business hours for the sole purpose of verifying
any reports and payments delivered under this Agreement. Such accountant shall
not disclose to the Auditing Party any information other than information
relating to accuracy of reports and payments delivered under this Agreement and
shall provide the Audited Party with a copy of any report given to the Auditing
Party. The Parties shall reconcile any underpayment or overpayment within
[*****] after the accountant delivers the results of the audit. The Auditing
Party shall bear the full cost of the audit unless, the audit performed under
this Section reveals an underpayment in excess of [*****] in any period, in
which case the Audited Party shall bear the full cost of such audit. Diversa may
exercise its rights under this Section only once every year and only with
reasonable prior notice to RPAN.

     5.7  [*****]. In the event RPAN wishes to exercise such option, the parties
shall negotiate in good faith [*****] which shall be based on, but not limited
to, [*****]. This [*****] shall also take into consideration [*****]

6.   Confidentiality

     6.1  Definition of Confidential Information. Confidential Information shall
mean any technical or business information, whether orally or in writing,
furnished by either party (the "Disclosing Party") to the other Party (the
"Receiving Party") in connection with this Agreement. Such Confidential
Information shall include, without limitation, the existence and terms of this
Agreement, the identity of an Enzyme, the Enzyme, any gene encoding such Enzyme,
if relevant, the use of an Enzyme, trade secrets, know-how, inventions,
technical data or specifications, testing methods, business or financial
information, research and development activities, product and marketing plans,
and customer and supplier information, including, but not limited to, such items
that become known to a Party during visits to the facilities of the other Party.

     6.2  Obligations.  The Receiving Party agrees that it shall:

          (a)  Maintain all Confidential Information in strict confidence,
except that the Receiving Party may disclose or permit the disclosure of any
Confidential Information to its directors, officers, employees, consultants and
advisors who are obligated to maintain the confidential nature of such
Confidential Information and who need to know such Confidential Information for
the purposes set forth in this Agreement;

          (b)  Use all Confidential Information solely for the purposes set
forth in, or as permitted by, this Agreement; and

          (c)  Allow its directors, officers, employees, consultants and
advisors to reproduce the Confidential Information only to the extent necessary
to effect the purposes set forth in this Agreement, with all such reproductions
being considered Confidential Information.

Each Party shall be responsible for any breaches of this Section 6.2. by any of
its directors, officers, employees, consultants and advisors.

     6.3  Exceptions.  The obligations of the Receiving Party under Section 6.2.
above shall not apply to any specific Confidential Information to the extent
that the Receiving Party can demonstrate that such Confidential Information:

                                      4.      *Confidential Treatment Requested
<PAGE>

          (a)  Was in the public domain prior to the time of its disclosure
under this Agreement;

          (b)  Entered the public domain after the time of its disclosure under
this Agreement through means other than an unauthorized disclosure resulting
from an act or omission by the Receiving Party or its directors, officers,
employees, consultants, advisors or agents;

          (c)  Was or is independently developed or discovered by the Receiving
Party without use of the Confidential Information, and which can be demonstrated
by written record;

          (d)  Is or was disclosed to the Receiving Party at any time, whether
prior to or after the time of its disclosure under this Agreement, by a third
party having no fiduciary relationship with the Disclosing Party and having no
obligation of confidentiality to the Disclosing Party with respect to such
Confidential Information; or

          (e)  Is required to be disclosed to comply with applicable laws or
regulations (such as disclosure to the SEC, the EPA, the FDA, or the United
States Patent and Trademark Office or to their foreign equivalents), or to
comply with a court or administrative order, provided that the Disclosing Party
receives prior written notice of such disclosure and that the Receiving Party
takes all reasonable and lawful actions to obtain confidential treatment for
such disclosure and, if possible, to minimize the extent of such disclosure.

     6.4  Survival of Obligations. The obligations set forth in Sections 6.1,
6.2 and 6.3 shall remain in effect after termination or expiration of this
Agreement for a period of [*****].

     6.5  Public Announcement. The Parties shall issue a joint press release
regarding this Agreement, the text of which shall be subject to mutual agreement
of the Parties. Except for the information disclosed in the joint press release,
neither party shall use the name of the other party or reveal the existence of
or terms of this Agreement in any publicity or advertising without the prior
written approval of the other party, except that (i) either party may use the
text of a written statement approved in advance by both parties without further
approval, and (ii) either party shall have the right to identify the other party
and to disclose the terms of this Agreement as required by applicable securities
laws or other applicable law or regulation, provided that the receiving party
takes reasonable and lawful actions to minimize the degree of such disclosure.

7.   Intellectual Property

     7.1  Ownership of Inventions. All intellectual property rights which are in
the possession of either party as of the Effective Date of this Agreement will
remain in the possession of that party. Ownership of inventions conceived of or
reduced to practice during the course of the collaboration (the "Inventions")
will be as follows:

Inventions involving Option Enzymes or Products.

     .  Diversa shall own all Inventions claiming compositions of matter, uses
or methods of or otherwise involving, any Option Enzyme or any derivative or
analog thereof (including any Derivative Enzyme).

     .  RPAN will own all Inventions claiming composition of matter uses or
methods of or otherwise involving the Base Catalyst and the Products.

Inventions involving Assays.

     .  Diversa will own all Inventions relating to any assays designed and/or
developed in the course of the collaboration that are conceived of solely by
Diversa.

                                      5.      *Confidential Treatment Requested
<PAGE>

     .  Diversa will own all Inventions relating to any assays designed and/or
        developed in the course of the collaboration that are conceived of
        jointly by Diversa and RPAN provided, however, that Diversa (i) will not
        use, or grant any third party the right to use, any such assays that
        incorporates or was designed and/or developed using any information or
        materials provided to Diversa by RPAN other than for research under this
        Agreement and (ii) will grant RPAN a free non-exclusive, non
        transferable license to use any such assays solely for RPAN's internal
        research purposes.

     .  RPAN will own all Inventions relating to any assays designed and/or
        developed in the course of the collaboration with Diversa that are
        conceived of solely by RPAN.

     7.2  Other Inventions. Except as specifically provided above, ownership of
all other Inventions will be determined in accordance with the rules of
inventorship under United States patent law.

8.   Patent Matters

     8.1  Responsibilities. Each party will be responsible for filing,
prosecuting, maintaining, defending and enforcing any patent applications,
patents and other intellectual property rights owned by such party, and the
parties will decide upon mutual agreement which party will be responsible for
filing, prosecuting, maintaining, defending and enforcing any patent
applications, patents and other intellectual property rights owned jointly by
the parties on a case by case basis.

     8.2  In the event that either party desires to abandon any patent
application, patent or other intellectual property right involving the [*****],
or if such party later declines responsibility for any such patent application,
patent or other intellectual property right, such party shall provide reasonable
prior written notice to the other party of such intention to abandon or decline
responsibility, and the other party shall have the right, at its own expense, to
file, prosecute, and maintain such patent application, patent or other
intellectual property right.

9.   Term and Termination

     9.1  Term. The term of this Agreement shall begin as of the Effective Date
and shall continue until the expiration of the Option Period, provided, however,
that if the Option is exercised, this Agreement shall continue until the last
day of the Royalty Term, unless earlier terminated as set forth below.

     9.2  Termination.

          9.2.1  Mutual Consent. This Agreement may be terminated at any time by
mutual written agreement of the Parties.

          9.2.2  Material Breach. In the event that a Party commits a material
breach of any of its obligations under this Agreement and such Party fails (i)
to remedy that breach within thirty (30) days after receiving written notice
thereof from the other Party or (ii) to commence dispute resolution pursuant to
Section 10.3, within thirty (30) days after receiving written notice of that
breach from the other Party, the other Party may immediately terminate this
Agreement upon written notice to the breaching Party.

     9.3  Disposition of Confidential Information. In the event of termination
or expiration of this Agreement, the Parties shall return or destroy all forms
of Confidential Information provided to them under this Agreement, within
[*****] after such termination or expiration, provided, however, that each Party
may retain one copy of such Confidential Information for record keeping purposes
only.

                                      6.      *Confidential Treatment Requested
<PAGE>

     9.4  Effect of Termination or Expiration. Termination or expiration of this
Agreement shall not relieve the parties of any obligation accruing prior to such
termination or expiration and shall not terminate any License granted or License
Agreement entered into prior to such termination or expiration. The provisions
of Sections 5.6, Articles 6 and 7 shall survive the expiration or termination of
this Agreement.

10.  Miscellaneous

     10.1 Relationship of Parties. Nothing in this Agreement is intended or
shall be deemed to constitute a partnership, agency, employer-employee or joint
venture relationship between the parties. No party shall incur any debts or make
any commitments for the other, except to the extent, if at all, specifically
provided herein.

     10.2 Governing Law. This Agreement shall be governed by and construed in
accordance with the laws of the State of New York other than those provisions
governing conflicts of law.

     10.3 Dispute Resolution Procedures. The Parties recognize that disputes as
to certain matters may from time to time arise which relate to either Party's
rights and/or obligations hereunder. It is the objective of the Parties to
establish procedures to facilitate the resolution of such disputes in an
expedient manner by mutual cooperation and without resort to litigation. To
accomplish this objective, the Parties agree to follow the procedures set forth
in this Section 10.3 if and when such a dispute arises between the Parties. If a
dispute arises between the Parties relating to the interpretation or performance
of this Agreement or the grounds for the termination thereof, the Parties agree
to hold a meeting, attended by individuals with decision-making authority
regarding the dispute, to attempt in good faith to negotiate a resolution of the
dispute prior to pursuing other available remedies. If, within [*****] after
such meeting, the Parties have not succeeded in negotiating a resolution of the
dispute, such dispute shall be finally settled only in San Diego, California, in
accordance with the rules and procedures of the American Arbitration Association
by three arbitrators knowledgeable as to biotechnology industry standards. Each
Party shall select one arbitrator [*****] after the institution of the
arbitration proceeding and the third arbitrator will be selected by mutual
agreement of the other two arbitrators within [*****] of the appointment of the
two arbitrators selected by the Parties. All of the arbitrators will be neutral,
impartial, independent of the Parties and others having any known interest in
the outcome; will abide by the ABA and AAA Cannons of Ethics for neutral
arbitrators, and will have no ex parte communications about the case or about
the appointment of the third arbitrator or the arbitrator's views on matters of
law with either Party in the appointing process or otherwise during the pendency
of the arbitration. The Parties shall bear the costs of arbitration equally
unless the arbitrators, pursuant to their right, but not their obligation,
require the non-prevailing Party to bear all or any unequal portion of the
prevailing Party's costs. The arbitrators shall prepare and deliver a written,
reasoned opinion conferring their decision within [*****] of the final
arbitration hearing. The arbitrators shall not have the power to award punitive
damages under this Agreement and such an award is expressly prohibited. The
decision of the arbitrators shall be final and binding on all of the Parties.
Judgment on the award so rendered may be entered in any court of competent
jurisdiction at the option of the successful Party. The rights and obligations
of the Parties to arbitrate any dispute relating to the interpretation or
performance of this Agreement or the grounds for the termination thereof shall
survive the expiration or termination of this Agreement for any reason.

     10.4  Counterparts. This Agreement may be executed in one or more
counterparts, each of which shall be deemed an original, and all of which
together shall be deemed to be one and the same instrument.

     10.5  Headings. All headings in this Agreement are for convenience only and
shall not affect the meaning of any provision hereof.

                                      7.      *Confidential Treatment Requested
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     10.6  Binding Effect. This Agreement and all rights and obligations
hereunder shall inure to the benefit of and be binding upon the Parties, their
Affiliates, and their respective lawful successors and assigns.

     10.7  Assignment. Except as otherwise provided herein, neither this
Agreement nor any interest hereunder will be assignable in part or in whole by
any Party without the prior written consent of the other Party; provided,
however, that either Party may assign this Agreement to any of its Affiliates or
to any successor by merger or sale of substantially all of its business to which
this Agreement relates This Agreement will be binding upon the successors and
permitted assigns of the Parties. Any assignment which is not in accordance with
this Section will be void.

     10.8  Notices. All notices, requests, demands and other communications
required or permitted to be given pursuant to this Agreement shall be in writing
and shall be deemed to have been duly given upon the date of receipt if
delivered by hand, recognized international overnight courier, confirmed
facsimile transmission, or registered or certified mail, return receipt
requested, postage prepaid to the following addresses or facsimile numbers:

     If to RPAN:                        If to Diversa:

     RPAN                               Diversa Corporation
     42 avenue Aristide Briand          10665 Sorrento Valley Road
     92160 Antony, France               San Diego, California 92121
     Attention: Research Director       Attention: Carolyn Erickson
     Copy: General Counsel -            Tel: (619) 623-5104
       Legal Department                 Fax: (619) 623-5180
     Tel: (33) 1-46-74-70-00
     Fax: (33) 1-40-96-96-96

Either party may change its designated address and facsimile number by notice to
the other party in the manner provided in this Section.

     10.9  Amendment and Waiver. This Agreement may be amended, supplemented, or
otherwise modified only by means of a written instrument signed by the Parties.
Any waiver of any rights or failure to act in a specific instance shall relate
only to such instance and shall not be construed as an agreement to waive any
rights or fail to act in any other instance, whether or not similar.

     10.10 Severability. In the event that any provision of this Agreement
shall, for any reason, be held to be invalid or unenforceable in any respect,
such invalidity or unenforceability shall not affect any other provision hereof,
and the parties shall negotiate in good faith to modify the Agreement to
preserve (to the extent possible) their original intent.

     10.11 Entire Agreement. This Agreement constitutes the entire agreement
between the parties with respect to the subject matter hereof and supersedes all
prior agreements or understandings between the parties relating to the subject
matter hereof.

     10.12 Regulatory Filings. RPAN shall have sole responsibility for making
all regulatory filings worldwide, including, without limitation, obtaining the
necessary approvals to market Products. Diversa will cooperate to provide
information required to make and maintain such filings, as appropriate,

                                      8.
<PAGE>

by either party by registered airmail or by telefax. In case of such termination
the terminating party will not be required to pay to the other party any
indemnity whatsoever.

Accepted and Agreed to:

<TABLE>
<S>                                               <C>
Rhone-Poulenc Animal Nutrition                    Diversa Corporation

Signature: /s/ Bernard Le Roux                    Signature: /s/ Jay M. Short
          ------------------------                          -----------------------------------------------------------
Name: Bernard Le Roux                             Name: Jay M. Short
     -----------------------------                     ----------------------------------------------------------------
Title: V.P. R & D RPAN                            Title: President Chief Executive Officer and Chief Technology Officer
      ----------------------------                      ---------------------------------------------------------------
Date: July 8, 1999                                Date: June 28, 1999
     -----------------------------                     ----------------------------------------------------------------
</TABLE>

                                      9.
<PAGE>

                           Exhibit A - Project Plan

                         PARTNERSHIP PROJECT R&D PLAN

          Discovery of a [*****] for the [*****] for use as a [*****]

Background:

[*****]

[*****]

                                    [*****]

[*****]

[*****]

1.   [*****]

2.   [*****]

3.   [*****]

4.   [*****]

5.   [*****]

RPAN: Project Performance and Delivery:

1.   [*****]

2.   [*****]

3.   [*****]

4.   [*****]

5.   [*****]

6.   [*****]

7.   [*****]

8.   [*****]

                                     10.      *Confidential Treatment Requested
<PAGE>

Diversa: Project Performance and Delivery:

1.   [*****]

2.   [*****]

Diversa Effort

[*****]

                                    [*****]

                                     11.       *Confidential Treatment Requested
<PAGE>

                                   Exhibit B

                RPAN's ENZYME PERFORMANCE ASSESSMENT PROCEDURE

Phase 1: [*****]

1.   [*****]

2.   [*****]

Approximate Time Required:

     [*****]
     [*****]

Phase II: [*****]
[*****]

3.   [*****]

Approximate Time Required:
     [*****]

Phase III: [*****]

1.   [*****]

Approximate Time Required:
     [*****]

Phase IV: [*****]

1.   [*****]

Approximate Time Required
     [*****]

Phase V: [*****]

1.   [*****]

2.   [*****]

Approximate Time Required:
     [*****]
     [*****]

                                     12.       *Confidential Treatment Requested
<PAGE>

                                   Exhibit C

                                    [*****]

                                    [*****]

                                     C-1.     *Confidential Treatment Requested
<PAGE>

                                   Exhibit D

                           LIST OF RELATED MOLECULES

                                    [*****]

                                     D-1.     *Confidential Treatment Requested<PAGE>

                                                                   EXHIBIT 10.21

                                               Confidential Treatment Requested
                                             Under 17 C.F.R. (S)(S) 200.80(b)(4)
                                                      200.83 and 230.406

                               LICENSE AGREEMENT

     This Agreement is made as of the 29/th/ day of March, 1999 by and between
Invitrogen Corporation, a corporation organized and existing under the laws of
the State of Delaware, with principal offices located at 1600 Faraday Avenue,
Carlsbad, California, 92008, ("Licensor") and Diversa Corporation, having its
principal place of business 10665 Sorrento Valley Road, San Diego, CA 92121
("Licensee").

1.   Definitions

     1.1  Affiliate means any business entity controlled by or under common
control with Licensee. For the purposes hereof, "control" shall mean, as to any
entity, effective ownership of greater than [*****] of the [*****].

     1.2  Licensed Patent Rights means the United States Patent Application
[*****] and [*****] licensed to Licensor, including all [*****] and [*****].
Said list will be periodically updated by Licensor.

     1.3  Licensed Products means any [*****] or any [*****].

     1.4  Net Sales means the dollar amount of [*****] of Licensed
Product(s) by Licensee and/or Affiliates, less [*****].

     1.5  Effective Date means the first date appearing above.

     1.6  Field Of Use means cloning of DNA inserts from uncultured organisms
only in conjunction with LICENSEE'S proprietary technology.  For purposes of
this paragraph "Licensee's proprietary technology" shall mean technology within
the ambit of any claim in an issued or pending patent claim of [*****] and any
[*****].

     1.7  Territory means the world.

2.   License Grant

     2.1  Licensor hereby grants to Licensee and Licensee accepts, subject to
the terms and conditions of this Agreement, an exclusive license to practice
Licensed Patent Rights in the Field Of Use in order to make, but not to have
made, use, and sell Licensed Products throughout the Territory for the term of
this Agreement.

                                   1.       *Confidential Treatment Requested

<PAGE>

     2.2  Additionally, Licensor hereby grants to Licensee and Licensee accepts,
subject to the terms and conditions of this Agreement, a non-exclusive license
to use Licensed Patent Rights for [*****] for Licensee's [*****]. "[*****]"
shall include [*****] and excludes [*****] Notwithstanding the foregoing,
Licensee shall be free to commercialize any product resulting from Licensee's
use of the Licensed Patent Rights in its research and discovery without
incurring any further royalty obligations.

     2.3  For purposes of Licensee's practice of the [*****], Licensor shall
provide Licensee annually with [*****] as set forth in Exhibit A hereto.
Licensee may purchase

additional quantities of [*****] needed subject to the pricing schedule set
forth in Exhibit A. In the event that Licensor sells [*****] to a third party
for a [*****] than that set forth on Exhibit A, then such [*****] shall be
extended to Licensee.

     2.4  Licensee shall have the right to extend the licenses granted herein to
Affiliates subject to the terms and conditions of this Agreement. Licensee shall
have no right to grant sublicenses hereunder.

3.   License Grant Fee

     3.1  In consideration for the license granted under paragraph 2.1, Licensee
agrees to pay to Licensor a [*****] license grant fee of [*****] United States
dollars payable within [*****] following the execution of this Agreement.

     3.2  Licensee further agrees to pay Licensor an annual license maintenance
fee in the sum of [*****] payable beginning [*****] from the end of the [*****]
following the EFFECTIVE DATE of this Agreement and continuing [*****] for the
life of this Agreement.

     3.3  In consideration of the license granted in paragraph 2.2, Licensee
shall [*****] grant to Licensor a first option for a license to make, use,
import, offer and sell in the research reagent market, as described below, at
least [*****], but no more than [*****] of Licensee's [*****]. Such enzymes
shall be selected from (i) Licensee's [*****] DNA modifying [*****] enzymes
[*****] or (ii) novel DNA modifying [*****] enzymes [*****] during the term of
the Agreement provided; however, that [*****] ((i) and (ii) are collectively
referred to below as [*****]). Prior to transfer, Licensee will provide [*****]
as well as other information if available, for the [*****] and [*****]. In the
event that Licensor finds that any such [*****] as represented by

                                      2.       *Confidential Treatment Requested
<PAGE>

Licensee, then Licensee shall provide [*****]. Licensee may, in its sole
discretion, also provide [*****] as they become available to Licensor, which
Licensor shall use solely for the purpose of [*****] which may be licensed
hereunder. Licensor may exercise its option on up to [*****] within [*****]. In
the event that, by the [*****] of this Agreement, either (i) Licensee has not
provided [*****] to Licensor for evaluation as set forth herein or (ii) Licensor
has not exercised its option to license at least [*****] as set forth hereunder,
then [*****].

For clarity, "first option" means [*****].

     3.4  Licensor may exercise such option by written notice to Licensee at any
time up to [*****] from the date Licensee provides [*****] to Licensor for
evaluation. Each [*****] shall be provided to Licensor by Licensee one time only
and each transfer shall be under the terms of a materials transfer agreement in
substantially the same form as Exhibit B hereto ("MTA"). Upon such notice of
option exercise by Licensor the parties shall enter into license negotiations
for the research reagent market. Such license shall not require any [*****] but
shall include, but not be limited to, a royalty rate of between [*****], a
provision that Licensee shall be named as the source of products licensed
thereunder in all [*****] and such other terms and conditions as are
commercially reasonable and customary in such agreements.

4.   License Term

     4.1  The license agreement will remain in effect the later of ten (10)
years or for so long as there are patents within License Patent Rights still in
force.

5.   Royalties

     5.1  Commencing on the Effective Date, Licensee shall pay to Licensor
during the term of this agreement a royalty of [*****] sold under the license
granted in paragraph 2.1.

     5.2  In the event that the royalty burden on any given Licensed Product is
increased due to the need for licensing additional components, the royalty
payable hereunder will be reduced by [*****] for each additional [*****] due to
third parties. Notwithstanding the foregoing, in no event shall the royalty due
Licensor be reduced to [*****] of the royalty specified in paragraph 5. 1.

                                      3.       *Confidential Treatment Requested
<PAGE>

6.   Reporting

     6.1  Licensee shall submit to Licensor within [*****] after the end of each
[*****] during the term of this Agreement, reports setting forth for the
preceding [*****] the following information:

          (1)  the number of each Licensed Product sold by Licensee and its
Affiliates;

          (2)  total billings for each Licensed Product;

          (3)  deductions applicable to determine the Net Sales thereof; and

          (4)  the amount of royalty due with respect to Licensee' sale of each
Licensed Product;

and with each such report pay the amount of royalty due. Such report shall be
certified as correct by an officer of Licensee.

     6.2  All payments due hereunder shall be payable in United States dollars.
Conversion of foreign currency to U.S. dollars shall be made at the conversion
rate existing in the United States as reported in the Wall Street Journal on the
last working day of each royalty reporting period.

     6.3  Late payments shall be subject to an interest charge of [*****].
Interest shall be calculated pro rata for lateness that includes [*****].

7.   Record Keeping

     7.1  Licensee shall keep, and shall require its Affiliates to keep accurate
and correct records of Licensed Products made, used or sold under this Agreement
appropriate to determine the amount of royalties due hereunder to Licensor. Such
records shall be retained for [*****] following a given reporting period. They
shall be available during normal business hours for

inspection at the expense of Licensor for the sole purpose of verifying reports
and payments hereunder. In the event that an inspection shows an under reporting
and underpayment in excess of [*****] for any [*****] period, then Licensee
shall pay the cost of such inspection as well as any additional sum that would
have been payable to Licensor had Licensee reported correctly, plus interest due
for lateness as specified above.

8.   Intellectual Property Rights

     8.1  All right, title and interest in and to all inventions, compositions,
and methods which cannot be practiced without LICENSED PATENT RIGHTS conceived
and/or reduced to practice solely by LICENSEE ("LICENSEE INVENTIONS") shall be
owned by Licensee.

                                      4.       *Confidential Treatment Requested
<PAGE>

     8.2  All right, title and interest in and to all inventions, compositions,
and methods dominated by LICENSED PATENT RIGHTS conceived and/or reduced to
practice solely by LICENSOR ("LICENSOR INVENTIONS") shall be owned by Licensor.

     8.3  All right, title and interest in and to all inventions dominated by
PATENT RIGHTS conceived and reduced to practice jointly by LICENSOR AND LICENSEE
("JOINT INVENTIONS") shall be owned jointly by Licensor and Licensee.

     8.4  Licensor will automatically receive a royalty free, paid-up non-
exclusive license to LICENSEE INVENTIONS for all purposes outside the Field Of
Use.

     8.5  Licensee will automatically receive a non-exclusive license to
LICENSOR INVENTIONS within the FIELD OF USE without further license grant fees,
but with running royalties payable according to Section 5.

     8.6  Exclusive licenses between the parties for Joint Inventions may be
granted and shall be negotiated in good faith.

9.   Infringement

     9.1  Licensee shall promptly notify Licensor of any suspected infringement
of any Licensed Patent Rights by a third party. Licensee and Licensor each shall
have the right to institute an action of infringement in the Field Of Use of the
Licensed Patent Rights in accordance with the following:

          (a)  If Licensor and Licensee agree to institute suit jointly, the
suit shall be brought in both their names, the out-of-pocket costs thereof shall
be borne equally, and any recovery or settlement shall be shared equally.
Licensee and Licensor shall agree on the manner in which they shall exercise
control over such action. Licensor may be represented, if it so desires, by
separate counsel of its own selection, the fees for which shall be paid by
Licensor.

          (b)  In the absence of an agreement to institute a suit jointly,
Licensor may institute suit and, at its option, join Licensee as a plaintiff.
Licensee shall execute all papers and perform such other acts as may be
reasonably required in the circumstances, at the expense of Licensor. Licensor
shall bear the entire cost of such litigation and shall be entitled to retain
the entire amount of any recovery or settlement.

          (c)  In the absence of an agreement to institute a suit jointly and if
Licensor notifies Licensee that it has decided not to join in or institute a
suit, as provided in (a) or (b) above, Licensee may institute a suit and, at its
option, join Licensor as a plaintiff.  Licensor shall

execute all papers and perform such other acts as may be reasonably required in
the circumstances, at the expense of Licensee. Licensee shall bear the entire
cost of such litigation and shall be entitled to retain the entire amount of any
recovery or settlement.

                                      5.       *Confidential Treatment Requested
<PAGE>

           (d)  If Licensor decides to institute suit, it shall notify Licensee
in writing within [*****]. Licensee's failure to notify Licensor in writing,
within [*****] after the date of Licensor's notice, that it will join in
enforcing the patent pursuant to the above provisions shall constitute an
assignment by Licensee to Licensor all rights, causes of action and damages
resulting from any infringement alleged in the suit and Licensor shall be
entitled to retain the entire amount of any recovery or settlement.

           (e)  Should either Licensee or Licensor commence a suit under the
above provisions and thereafter elect to abandon same, it shall give timely
notice to the other party who may, at its discretion, continue prosecution of
the suit. The parties will negotiate in good faith to allocate the expenses and
proceeds of such suit.

     9.2   In the event that a declaratory judgment action alleging invalidity
of any of the Licensed Patent Rights shall be brought against Licensee or
Licensor, then Licensor, at its sole option, shall have the right to intervene
and take over the sole defense of such action at its own expense. Licensor shall
have exclusive control of any enforcement of Licensed Patent Rights outside the
Field Of Use.

10.  Termination

     10.1  The obligation to pay royalties on a Licensed Product shall expire
when all patents within Licensed Patent Rights covering that Licensed Product
have expired in the jurisdiction where the Licensed Product is sold to its
ultimate consumer.

     10.2  In the event Licensee fails to make payments due hereunder, Licensor
shall have the right to terminate this Agreement upon ninety (90) days written
notice, unless within the ninety (90) day notice period Licensee makes all
outstanding payments plus interest.

     10.3  In the event that Licensee shall be in default in the performance of
any obligation under this Agreement (other than as provided in 10.2 above), and
if the default has not been remedied within ninety (90) days after the date of
notice in writing specifying the nature of such default, Licensor may terminate
this Agreement immediately by further written notice to Licensee.

     10.4  This Agreement and all licenses granted under it shall terminate
automatically should Licensee commit any act of bankruptcy, become insolvent,
file a petition under any bankruptcy or insolvency act, or have any such
petition filed against it, or make any assignment for the benefit of its
creditors.

     10.5  Licensee shall have the right to terminate this Agreement for any
reason or no reason upon ninety (90) days written notice to Licensor.

     10.6  In the event of any termination or expiration, Licensee shall have
the right to continue selling Licensed Products until finished goods in
existence on the date of final notice of termination are sold, or [*****]
whichever is sooner, provided however that such right shall not apply to
voluntary termination under paragraph 10.5. Such sales will be subject to the

                                      6.       *Confidential Treatment Requested
<PAGE>

provisions of the Agreement. Following the [*****] or immediately upon the
effective date of a termination under paragraph 10.5, Licensee will destroy all
remaining materials which may be used to practice Licensed Patent Rights, or
which were produced under licenses granted herein and an officer of Licensee
shall certify such destruction to Licensor in writing under oath.

11.  Breach And Cure

     11.1  In addition to applicable legal standards, Licensee shall be in
material breach of this Agreement for failure to pay any fees under Section III
or any royalties pursuant to Section V.

     11.2  Either party shall have the right to cure its material breach. The
cure shall be effected within a reasonable time but in no event later than
[*****] after written notice of breach given by the party claiming breach and
specifying the nature of the breach.

12.  Warranty

     12.1  Licensor represents and warrants it has the authority to issue the
licenses granted herein under License Patent Rights. Licensor warrants that, as
of Effective Date, it has disclosed to Licensee any claims, rights or
allegations by third parties of which it is aware which may conflict or overlap
with License Patent Rights. Licensor does not warrant the validity of the
License Patent Rights licensed hereunder and makes no representation whatsoever
with regard to the scope of the License Patent Rights, or that such License
Patent Rights may be exploited by Licensee or an Affiliate of Licensee without
infringing other patents. Licensor EXPRESSLY DISCLAIMS ANY OTHER IMPLIED OR
EXPRESS WARRANTIES AND MAKES NO EXPRESS OR IMPLIED WARRANTIES OF MERCHANTABILITY
OR FITNESS FOR ANY PARTICULAR PURPOSE OF THE LICENSED PATENT RIGHTS OR LICENSED
PRODUCTS CONTEMPLATED BY THIS Agreement.

13.  Indemnification

     13.1  Licensee shall indemnify, defend and hold harmless Licensor against
any liability, damage, loss or expense (including reasonable attorneys' fees and
expenses of litigation) incurred by or imposed upon Licensor in connection with
any claim, suit, action, demand or judgment arising out of any theory of product
liability (including, but not limited to, actions in the form of tort, warranty,
or strict liability) relating to any product, process or service made, used or
sold pursuant to any right or license granted under this Agreement.

14.  Publicity

     14.1  All public announcements regarding the existence or terms of this
Agreement shall be coordinated between Licensor and Licensee and shall be made
only by mutual agreement.

15.  Notices

     15.1  Notices regarding termination of this Agreement shall be made by
certified mail, return

                                      7.       *Confidential Treatment Requested
<PAGE>

receipt requested or by a courier service requiring a signature upon receipt.

     15.2  All other notices or documents to be given hereunder may be sent in a
pre-paid letter to the address of the relevant party set out in this Agreement
or to such other address as the parties may designate in writing for the
purposes of this part. Any notice sent by U.S. Mail shall be deemed (in the
absence of evidence of earlier receipt) to have been delivered [*****] after
dispatch.

16.  Miscellaneous

     16.1  This Agreement shall be governed by California law applicable to
agreements made and to be performed in California.

     16.2  This Agreement shall be binding on the parties hereto and upon their
respective heirs, administrators, successors and assigns. This Agreement may not
be assigned by either party without the written consent of the other party,
except that Licensee may assign this Agreement as part of a sale of transfer of
all, or substantially all, of the assets of Licensee to which the Agreement
relates.

     16.3  This Agreement sets forth the entire agreement between the parties
concerning the subject matter hereof and merges all previous agreements or
communications.

     16.4  Should any provision of this Agreement be held invalid, illegal or
unenforceable by a court of competent jurisdiction, such provision shall be
considered void. All other provisions, rights and obligations shall continue
without regard to such holding.

     16.5  No amendment or modification of this Agreement shall be valid or
binding upon the parties unless made in writing and signed by both parties.

     16.6  A waiver by either party of a breach by the other of any term of this
Agreement shall not prevent the subsequent enforcement of that term and shall
not be deemed a waiver of any subsequent, prior or continuing breach.

In Witness Whereof, the Licensor and Licensee have executed this Agreement as of
the Effective Date.

Licensor, by:                                   Licensee, by:

/s/ Warner Broadus                              /s/ Carolyn Erickson
-------------------------------------           -----------------------------
Signature                                       Signature

Warner Broadus                                  Carolyn Erickson
-------------------------------------           -----------------------------
Printed Name                                    Printed Name

General Counsel & Assistant Secretary           Director, IP
-------------------------------------           -----------------------------
Title                                           Title

                                      8.       *Confidential Treatment Requested

<PAGE>

                                   EXHIBIT A

Included in the Agreement: [*****].

Licensee may purchase [*****].

                                     A-1.      *Confidential Treatment Requested

<PAGE>

                                   EXHIBIT B

                         Materials Transfer Agreement

Effective as of ____________, 1999, this Agreement ("Agreement") is made and
entered into by and between Diversa Corporation, a Delaware corporation with
headquarters at 10665 Sorrento Valley Road, San Diego, CA 92121 (hereinafter
"Diversa"), and _____________, a ___________________ corporation with
headquarters at ____________________________ (hereinafter "Recipient"),
collectively known as "The Parties."

WHEREAS, Diversa will provide Recipient with [*****] as set forth in Exhibit A
attached hereto and hereinafter referred to as "Material";

WHEREAS, Recipient desires to evaluate the Material;

WHEREAS, Recipient is willing to receive the Material pursuant to the terms and
conditions of this Agreement;

WHEREAS, Diversa agrees to provide the Material to Recipient pursuant to the
terms and conditions of this Agreement;

NOW THEREFORE, in consideration of the mutual promises and covenants herein
contained, the Parties mutually agree to the following terms:

1.   Diversa will provide to Recipient the following Material: Diversa shall
     provide Recipient with [*****] set forth in Exhibit A to allow Recipient to
     [*****].

2.   Recipient agrees that the Material shall be used solely for the purpose of
     evaluation of the potential usefulness of the Material in Recipients
     processes. The Material shall not be used in research that is subject to
     consulting or licensing obligations of any third party without the prior
     written consent of Diversa.

3.   The Material delivered hereby is experimental in nature. DIVERSA MAKES NO
     WARRANTIES, EXPRESS OR IMPLIED, INCLUDING ANY WARRANTY OF MERCHANTABILITY
     OR FITNESS FOR A PARTICULAR PURPOSE.  Diversa makes no representation that
     the use of the Material will not infringe any patent or proprietary rights
     of third parties.

4.   Recipient agrees that the Material shall not be distributed to any third
     party or entity, except affiliates and subsidiaries of Recipient, without
     the prior written consent of Diversa.

5.   Recipient agrees that dissemination of the Material shall be limited to
     those employees of Recipient with a special need to know and work with such
     Material.

6.   Information transferred under this Agreement, including but not limited to
     the Material and all information related to the Material, shall be
     "Confidential Information". Recipient shall not disclose to third parties
     any Confidential Information received from Diversa

     hereunder, provided, however, that Recipient shall have no objections to
     Diversa with respect to the use, or disclosure to others not party to this
     Agreement, of such information which:

     a)   prior to disclosure was known to or in the possession of Recipient as
          evidenced by its written records; or

     b)   is or becomes publicly known during the term of this Agreement, other
          than through a breach of Recipient's obligations hereunder; or

     c)   is received from a third party having no obligations of
          confidentiality to Diversa hereunder; or

     d)   is developed by Recipient independently of any disclosures made under
          this Agreement as evidenced by its written records; or

                                     B-1.      *Confidential Treatment Requested
<PAGE>

     e)   is required by law or bona fide legal process to be disclosed,
          provided that Recipient takes all reasonable steps to restrict and
          maintain the confidentiality of such disclosure and provides
          reasonable notice to Diversa; or

     f)   is authorized to be released in a written release by Diversa.

7.   Recipient agrees to return all documents, samples, and other tangible items
     containing or representing Confidential Information, and all copies
     thereof, erase or destroy all Confidential Information contained in
     computer memory or data storage apparatus, and certify in writing that it
     has complied with the terms of this Paragraph 7, provided that Recipient
     may, upon written notice to Diversa, retain in confidence a single copy of
     that Confidential Information in the offices of Recipient's legal counsel
     for legal records.

8.   Recipient acknowledges that all right, title and interest in and to the
     Materials belongs solely to Diversa.  Recipient shall not modify the
     Materials in any way, reverse engineer the Materials, use the Materials for
     reproduction, offer the Materials or any derivative thereof for resale, use
     the Materials in any form of human or animal testing.

9.   [*****].

10.  No rights under any intellectual property of Diversa or rights in any other
     Material or Confidential Information that could not have been attained, but
     for this Material, is granted or implied as a result of providing this
     Material to Recipient.

11.  None of the Material provided hereunder shall be used for any commercial
     development directly or indirectly unless a license granting the same is
     executed between the Parties. Recipient agrees that the Material, method of
     using the Material, or any other material that could not have been made but
     for the Material, shall not be sold or otherwise transferred to any third
     party.

12.  Diversa shall not be liable for any use of the Material or related know-how
     and Recipient agrees to indemnify, defend, and hold harmless Diversa and
     its officers, directors,

     shareholders, employees, agents, and representatives (collectively
     "Indemnitee") against all liability, demands, claims, costs, losses,
     damages, recoveries, settlements, and expenses (including interest,
     penalties, attorney fees, accounting fees, expert witness fees, costs, and
     expenses) incurred by Indemnitee, known or unknown, contingent or
     otherwise, directly or indirectly arising from or related to this Agreement
     or the use of the Material or related know-how hereunder.

13.  This Agreement and rights thereunder shall not be assigned or transferred,
     directly or indirectly, in whole or in part by the Parties.

14.  This Agreement shall be effective for five (5) years from the date set
     forth above.

15.  The Parties may terminate this Agreement on [*****] written notice;
     however, upon termination of this Agreement, nothing herein shall be
     construed to release the Parties from any obligation that matured prior to
     the effective date of such termination. In the event this Agreement is
     terminated for any reason, the rights and obligations of Paragraphs 6, 7,
     8, 9, 10, 11 and 12 shall survive termination of this Agreement.

16.  The Parties represent and warrant that each has the authority to undertake
     the obligations set forth in this Agreement without breaching or violating
     any contractual or statutory obligation owed to another.

                                     B-2.      *Confidential Treatment Requested

<PAGE>

17.  The provisions of this Agreement are severable and in the event any
     provisions of this Agreement are determined to be held invalid or
     unenforceable under any controlling body of law, such invalidity or
     unenforceability shall not in any way affect the validity and
     enforceability of the remaining provisions hereof.

18.  This Agreement constitutes the entire agreement and understanding between
     the Parties concerning the subject matter thereof. It merges with and
     supersedes all previous agreements and understandings between the Parties.

19.  This Agreement shall be construed in accordance with the laws of the State
     of California without regard to its conflict of laws principles.

20.  After receipt of the executed Agreement, Diversa will arrange to provide
     Recipient with the Materials.

IN WITNESS WHEREOF, the Parties have, through duly authorized representatives,
executed this Agreement, effective as of the date set forth above.

                                        Diversa Corporation

___________________________             ________________________________________
Name                                    Carolyn Erickson
                                        Director, Intellectual Property

Title:____________________

                                  B-3.

<PAGE>

                                   EXHIBIT A

                                TO BE PROVIDED

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