<PAGE>
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                                 UNITED STATES
                       SECURITIES AND EXCHANGE COMMISSION

                             WASHINGTON, D.C. 20549
                            ------------------------
                                  FORM 10-K/A
                                AMENDMENT NO. 1

<TABLE>
<C>        <S>
   /X/     ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE
           SECURITIES EXCHANGE ACT OF 1934
</TABLE>

                  FOR THE FISCAL YEAR ENDED DECEMBER 31, 1999

<TABLE>
<C>        <S>
   / /     TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE
           SECURITIES EXCHANGE ACT OF 1934
</TABLE>

        FOR THE TRANSITION PERIOD FROM ______________ TO ______________

                        COMMISSION FILE NUMBER: 0-12177
                            ------------------------
                          BIONOVA HOLDING CORPORATION

             (Exact Name of Registrant as Specified in its Charter)

<TABLE>
<S>                                            <C>
               DELAWARE                                     75-2632242
       (State of incorporation)                (I.R.S. Employer Identification No.)

         6701 SAN PABLO AVENUE                                94608
          OAKLAND, CALIFORNIA                               (Zip Code)
    (Address of principal executive
               offices)
</TABLE>

       REGISTRANT'S TELEPHONE NUMBER, INCLUDING AREA CODE: (510) 547-2395

          SECURITIES REGISTERED PURSUANT TO SECTION 12(b) OF THE ACT:

                     COMMON STOCK, PAR VALUE $.01 PER SHARE
                                (Title of class)

        SECURITIES REGISTERED PURSUANT TO SECTION 12(g) OF THE ACT: NONE
                            ------------------------

    Indicate by check mark whether the registrant (1) has filed all reports
required to be filed by Section 13 or 15(d) of the Securities Exchange Act of
1934 during the preceding 12 months (or for such shorter period that the
registrant was required to file such reports), and (2) has been subject to such
filing requirements for the past 90 days. Yes /X/  No / /

    Indicate by check mark if disclosure of delinquent filers pursuant to Item
405 of Regulation S-K is not contained herein, and will not be contained, to the
best of Registrant's knowledge, in definitive proxy or information statements
incorporated by reference in Part III of this Form 10-K or any amendment to this
Form 10-K. Yes / /  No /X/

    Aggregate market value of Common Stock held by non affiliates as of
April 26, 2000: $16,352,400

    Number of shares of Common Stock outstanding as of April 26, 2000:
23,588,031

                      DOCUMENTS INCORPORATED BY REFERENCE

                                      NONE

--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
<PAGE>
    This Form 10-K/A is being filed to report information previously omitted
from the Company's Form 10-K pursuant to G(3) of the General Instructions to
Form 10-K.

                               TABLE OF CONTENTS

<TABLE>
<CAPTION>
                                                                            PAGE
                                                                          --------
<S>         <C>                                                           <C>
PART III................................................................      3

 ITEM 10.   DIRECTORS AND EXECUTIVE OFFICERS OF THE COMPANY.............      3

 ITEM 11.   EXECUTIVE COMPENSATION......................................      4

 ITEM 12.   SECURITY OWNERSHIP OF CERTAIN BENEFICIAL OWNERS AND
            MANAGEMENT..................................................     10

 ITEM 13.   CERTAIN RELATIONSHIPS AND RELATED PARTY TRANSACTIONS........     11
</TABLE>

                                       2
<PAGE>
                                    PART III

ITEM 10. DIRECTORS AND EXECUTIVE OFFICERS OF THE COMPANY

    Certain information with respect to persons who are or may be deemed to be
executive officers of Bionova Holding Corporation ("Bionova Holding" or the
"Company") is set forth under the caption "Executive Officers of the Company" in
Part I of the Company's annual report on Form 10-K for the year ended
December 31, 1999.

    Certain background information regarding the current directors is set forth
below. Each director's term of office will expire on the date of the Company's
annual meeting of stockholders for the year 2000.

    EVELYN BEREZIN--Ms. Berezin (age 74) has been a venture capital consultant
since 1987 and was President of Greenhouse Management Corporation, the general
partner of a venture capital firm, from 1981 until 1987. Ms. Berezin is a
director of Standard Microsystems Corporation and served as a director of CIGNA
Corp. until 1995. Ms. Berezin has served as a director of the Company since
1996.

    DR. PETER DAVIS--Dr. Davis (age 55) is a member of the Executive Committee
of Pulsar Internacional, S.A. de C.V. ("Pulsar"), an affiliate of Savia, S.A. de
C.V. ("Savia"), and serves as a director of Seminis, Inc. ("Seminis"), a company
that develops, produces and markets fruit and vegetable seeds. Dr. Davis was
previously a professor at the Wharton School, where he also served as Director
of the Wharton Applied Research Center and Director of Executive Education.
Dr. Davis has served as a director of the Company since 1996.

    CARLOS HERRERA--Mr. Herrera (age 59) is the Director of Business Development
of Agromod, S.A. de C.V. He served as the Chief Executive Officer of the Company
from July 1996 through September 1997. Mr. Herrera has served as the Managing
Director (Chief Executive Officer) of Bionova Mexico since 1993. He is an
alternate director of Savia. Mr. Herrera has served as a director of the Company
since 1996.

    BERNARDO JIMENEZ--Mr. Jimenez (age 46) became the Chief Executive Officer of
the Company in October 1997. He is also the Chief Operating Officer of the
agrobiotechnology division of Savia, and serves as a director of Seminis and
Savia. From 1993 to 1996, he served as the head of the Industrial Banking
Division at the Vector Group, a financial services company in Mexico which is
affiliated with Savia, the Vice President of New Business Development for
Pulsar, and the Chief Financial Officer of Savia. From 1975 to 1993, he held
various positions in finance and management at Grupo Industrial Alfa, S.A. de
C.V. Mr. Jimenez has served as a director of the Company since 1996.

    DR. GERALD D. LAUBACH--Dr. Laubach (age 74) was the President of
Pfizer, Inc., a pharmaceutical company, from 1972 to 1991. He served as a
director of CIGNA Corp. and Millipore Corp. until 1996. Dr. Laubach has served
as a director of the Company since 1996.

    EUGENIO NAJERA--Mr. Najera (age 52) has been in charge of new business
development at Savia since August 1997. Prior to that time, he was the Chief
Executive Officer of Cigarrera La Moderna, S.A. de C.V. He is a director of
Savia and Seminis. Mr. Najera has served as a director of the Company since
1998.

    ALEJANDRO PEREZ--Mr. Perez (age 51) has been the Vice President of
Diversification of Pulsar since 1991. He formerly served as a director of
WebLink Wireless, Inc., and currently serves as a director of several
privately-held technology-based companies affiliated with Pulsar. Mr. Perez has
served as a director of the Company since 1998.

    DR. ELI SHLIFER--Dr. Shlifer (age 68) has been a director of Seminis since
January 1997. Dr. Shlifer has been a member of the executive committee of Pulsar
since 1989 and has served as an advisor to many companies affiliated with
Pulsar. Dr. Shlifer has served as a director of the Company since 1999.

    DR. CHRISTOPHER R. SOMERVILLE--Dr. Somerville (age 52) is a member of the
faculty in the Department of Biological Sciences at Stanford University and the
Director of the Department of Plant Biology at the Carnegie Institution of
Washington, a private research institute located on the Stanford University
campus.

                                       3
<PAGE>
Prior to moving to Stanford in 1994, Dr. Somerville held faculty positions at
the University of Alberta and Michigan State University. Dr. Somerville is a
co-founder and member of the Scientific Advisory Board of Mendel
Biotechnologies, Inc., an agriculturally-oriented biotechnology company founded
in 1997. Dr. Somerville has served as a director of the Company since 1998.

SECTION 16(a) BENEFICIAL OWNERSHIP REPORTING COMPLIANCE

    Section 16(a) of the Securities Exchange Act of 1934, as amended, requires
directors and officers of the Company, and persons who beneficially own more
than 10 percent of the Company's Common Stock, par value $0.01 per share
("Common Stock"), to file with the SEC initial reports of ownership and reports
of changes in ownership of the Common Stock. Directors, officers and more than
10 percent stockholders are required by SEC regulations to furnish the Company
with copies of all Section 16(a) forms they file. To the Company's knowledge,
based solely on a review of the copies of such reports furnished to the Company
and written representations that no other reports were required, during the year
ended December 31, 1999, and except that the initial statement of beneficial
ownership of securities on Form 3 of Dr. Shlifer was inadvertently filed late,
all Section 16(a) filing requirements applicable to its directors, officers and
more than 10 percent beneficial owners were complied with.

ITEM 11. EXECUTIVE COMPENSATION

    The following table sets forth certain information with respect to annual
and long-term compensation paid or awarded to the Company's current chief
executive officer and to the other four most highly-paid executive officers of
the Company (together, the "Named Executive Officers") for or with respect to
the fiscal years ended December 31, 1999, 1998, and 1997.

<TABLE>
<CAPTION>
                                                ANNUAL COMPENSATION                     COMPENSATION AWARDS           OTHER
                                 --------------------------------------------------   ------------------------   ----------------
                                                                                      RESTRICTED   SECURITIES
           NAME AND                           BASE                   OTHER ANNUAL       STOCK      UNDERLYING       ALL OTHER
      PRINCIPAL POSITION           YEAR     SALARY($)   BONUS($)   COMPENSATION($)    AWARDS($)    OPTIONS(#)    COMPENSATION($)
-------------------------------  --------   ---------   --------   ----------------   ----------   -----------   ----------------
<S>                              <C>        <C>         <C>        <C>                <C>          <C>           <C>
Bernardo Jimenez...............    1999      469,940         --(5)       9,280(6)         0             0                 0
  Chief Executive Officer(1)       1998      413,600    114,860          9,330(6)         0             0                 0
                                   1997       51,000          0              0            0             0                 0

Jorge Fenyvesi.................    1999      280,000         --(5)     182,670(7)         0             0                 0
  Executive Vice President(2)      1998      280,000    130,900        188,010(7)         0             0                 0
                                   1997      120,000    117,000        109,200(7)         0             0                 0

Arthur H. Finnel...............    1999      325,400         --(5)      12,890(6)         0             0             4,570(9)
  Executive Vice President,        1998      295,640     71,130         12,590(6)         0             0             2,120(9)
  Treasurer and Chief              1997      271,810     75,810         11,290(6)         0             0             2,050(9)
  Financial Officer

Dr. John R. Bedbrook...........    1999      105,170         --          7,300            0             0             5,000(9)
  Executive Vice President(3)      1998      260,620    135,670         24,940(8)         0             0             4,800(9)
                                   1997      209,100     88,125              0            0             0             4,750(9)

Omar Diaz......................    1999      284,600         --(5)      20,740(6)         0             0             4,150(9)
  President of International       1998       93,680     32,350              0            0             0                 0
    Produce Holding Company(4)
</TABLE>

------------------------------

(1) Mr. Jimenez became Chief Executive Officer of the Company as of October 1,
    1997. Only the portion of his compensation related to his services on behalf
    of the Company and its subsidiaries has been included here.

(2) Mr. Fenyvesi joined the Company in July, 1997.

(3) Only a portion of Dr. Bedbrook's services while he was with the Company
    during 1999 was directed at the business of Bionova Holding. The other
    portion of his time was spent on services to Bionova Holding's indirect
    parent company, Savia, S.A. de C.V. Only the portion of his compensation
    related to his services on behalf of the Company and its subsidiaries has
    been included here. Dr. Bedbrook left the Company in November, 1999.

(4) Mr. Diaz joined the Company in September, 1998

                                       4
<PAGE>
(5) Bonuses earned for 1999 performance had not been determined nor awarded as
    of the time of the issuance of this 10-K Amendment.

(6) Represents certain vacation and other allowances paid on behalf of the
    employees.

(7) Includes $87,510, $89,330 and $35,640 in Federal and state income taxes paid
    on behalf of Mr. Fenyvesi with respect to certain benefits he received in
    1999, 1998 and 1997, respectively. Includes certain expatriate bonuses,
    sign-on bonuses and education allowances in 1999, 1998 and 1997 amounting to
    $50,000, $50,000 and $72,350, respectively.

(8) Includes auto allowances, vacation allowances, and Federal and state income
    taxes paid on these benefits in the amounts of $9,120, $8,440 and $7,380,
    respectively.

(9) Represents contributions made by DNA Plant Technology Corporation to its
    401(k) Retirement and Savings Plan.

    All of Mr. Jimenez's compensation, and a portion of the compensation paid to
Messrs. Finnel and Diaz, is paid in Mexican pesos. The amounts shown above have
been converted to dollars based on a weighted average of the peso/dollar
exchange rate during the relevant time periods. The portion of the base salaries
of these individuals paid in pesos was increased in 1999 consistent with the
rate of inflation in Mexico which, due to the relative stability of the
peso/dollar exchange rate in 1999, resulted in the salary increases shown above.

    In connection with the separation of Dr. Bedbrook as an Executive Officer of
the Company in November, 1999, the Company agreed to make severance payments to
him equating to six months of base salary. Dr. Bedbrook received $38,460 of
severance payments in 1999 and will receive an additional $86,540 in the year
2000.

                             OPTION GRANTS IN 1999

    The following table contains information concerning the grant of stock
options made during the fiscal year ended December 31, 1999 to the Named
Executive Officers.

<TABLE>
<CAPTION>
                                   NUMBER OF      PERCENT OF
                                  SECURITIES     TOTAL OPTIONS
                                  UNDERLYING      GRANTED TO     EXERCISE
                                    OPTIONS      EMPLOYEES IN      PRICE     EXPIRATION       GRANT DATE
NAME                             GRANTED(#)(1)      1999(2)      ($/SHARE)      DATE      PRESENT VALUE($)(3)
----                             -------------   -------------   ---------   ----------   -------------------
<S>                              <C>             <C>             <C>         <C>          <C>
Bernardo Jimenez...............     103,800          26.4%         3.25      04/28/2009        $301,020
Jorge Fenyvesi.................      39,200          10.0%         3.25      04/28/2009        $113,680
Arthur Finnel..................      37,900           9.7%         3.25      04/28/2009        $109,910
John Bedbrook(4)...............      35,000           8.9%         3.25      04/28/2009        $101,500
Omar Diaz......................      32,500           8.3%         3.25      04/28/2009        $ 94,250
</TABLE>

------------------------

NOTES:

1.  All of these options were granted on April 28, 1999 and first become
    exercisable in annual one-fourth installments, beginning one year from the
    grant date, and have a ten-year term.

2.  The percentages in the table for the stock options granted in 1999 are based
    on a total of 392,600 stock options granted in 1999 to employees of the
    Company, all of which were granted on the same terms as described in
    footnote 1.

3.  The grant date present values shown in the table for the stock options are
    determined using the Black-Scholes option pricing model. The assumptions
    used in calculating the Black-Scholes present value of approximately $2.90
    per option for new option grants were as follows: dividend yield of 0%,
    expected volatility of 114%, risk free interest rate of 5.2%, and an
    expected life of 7 years.

    The Black-Scholes option pricing model was developed for use in estimating
    the fair value of traded options that have no vesting restrictions and are
    fully transferable. In addition, option pricing models require the use of
    highly subjective assumptions, including the expected stock price
    volatility. Because

                                       5
<PAGE>
    the Corporation's employee stock options have characteristics significantly
    different from those of traded options, and because changes in the
    subjective assumptions can materially affect the fair value estimates, the
    Black-Scholes model does not necessarily provide a reliable single measure
    of the fair value of the Corporation's employee stock options. The amount
    realized from an employee stock option ultimately depends on the market
    value of the common stock on the date of exercise.

4.  Consistent with the terms of the Long-Term Incentive Plan, Dr. Bedbrook's
    options expired in February, 2000, three months after his separation from
    the Company.

                    AGGREGATED OPTION EXERCISES IN 1999 AND
                             YEAR-END OPTION VALUES

<TABLE>
<CAPTION>
                                                                NUMBER OF SECURITIES
                                                                     UNDERLYING             VALUE OF UNEXERCISED IN-
                                                               UNEXERCISED OPTIONS AT               THE-MONEY
                                                                     YEAR-END(#)             OPTIONS AT YEAR-END($)
                                   SHARES                    ---------------------------   ---------------------------
                                 ACQUIRED ON      VALUE
NAME                             EXERCISE(#)   REALIZED($)   EXERCISABLE   UNEXERCISABLE   EXERCISABLE   UNEXERCISABLE
----                             -----------   -----------   -----------   -------------   -----------   -------------
<S>                              <C>           <C>           <C>           <C>             <C>           <C>
Bernardo Jimenez...............       0             0             0           103,800            0              0
Jorge Fenyvesi.................       0             0             0            39,200            0              0
Arthur Finnel..................       0             0             0            37,900            0              0
John Bedbrook..................       0             0             0            35,000            0              0
Omar Diaz......................       0             0             0            32,500            0              0
</TABLE>

COMPENSATION OF DIRECTORS

    Directors who are not officers of the Company or any of its affiliates
receive an annual retainer of $6,000, a fee of $1,000 for each Board meeting
attended and a fee of $500 for each committee or telephone meeting in which the
director participates. The Company also reimburses directors for travel, lodging
and related expenses they incur in attending Board and committee meetings.

COMPENSATION COMMITTEE INTERLOCKS AND INSIDER PARTICIPATION

    The members of the Compensation Committee are Evelyn Berezin and
Dr. Christopher Somerville, both of whom are non-employee directors. The
Company's Chief Executive Officer, Bernardo Jimenez, is a director of Savia.

COMPENSATION COMMITTEE REPORT ON EXECUTIVE COMPENSATION

    In accordance with the rules of the Securities and Exchange Commission (the
"Commission"), the following report of the Compensation Committee of the Board
of Directors and the information herein under "Performance Graph" shall not be
deemed to be "soliciting material" or to be "filed" with the Commission, and
such information shall not be deemed to be incorporated by reference into any
statements or reports filed by the Company with the Commission that do not
specifically incorporate such information by reference, notwithstanding the
incorporation by reference of this Form 10-K/A into any such statements or
reports.

            REPORT OF COMPENSATION COMMITTEE ON ANNUAL COMPENSATION

    The Compensation Committee (the "Committee") of the Board of Directors of
the Company is responsible for (i) administering the Company's stock option and
stock incentive plans, (ii) recommending to the Board matters pertaining to
employment agreements, salaries and bonuses for the Company's executive officers
and contributions to any of the Company's or its subsidiaries' 401(k) Investment
Plans, and (iii) carrying out any other duties delegated to the Committee by the
Board from time to time. The

                                       6
<PAGE>
goal of the Company's executive compensation policy is to ensure that an
appropriate relationship exists between executive pay and performance against
the Company's objectives and that the Company can attract, motivate and retain
key executives.

    The Company's executive compensation philosophy is as follows: that
(i) executive compensation packages should be designed in a manner whereby the
Company can attract and retain high quality executive talent needed to ensure
the short-term and long-term success of both its fresh produce agricultural and
distribution business as well as its technology development and research
activities and businesses, (ii) significant incentives, both short-term and
long-term, should become an increasing portion of executive compensation and
awarded based on both company and individual performance, and (iii) an alignment
of interests between executives and shareholders will be created through
compensation structures that share the rewards and risks of strategic
decision-making and performance.

    The Committee has determined that it will collect and analyze survey data of
a competitive peer group of companies at least every two years. In 1999, the
Committee reviewed all of the compensation arrangements of the current group of
executive officers. The Committee determined from this review, the specifics of
which are clarified below, that the compensation of these individuals was
somewhat higher than the mid-point of the competitive set, but consistent with
the Company's needs at this point in its development to attract and retain
individuals with the capabilities to drive the Company forward in this very
rapidly changing and complex business environment.

    The key components of executive compensation are discussed below.

    BASE SALARY.  The Company has determined that it will annually set base
salary targets for its executive officers at levels competitive with persons
holding comparable positions at other companies in the Company's comparison set.
In reviewing the base salaries for executive officers of the Company against
this objective, the Committee reviewed executive compensation surveys with
companies in its major fields of business, which included fresh produce and
biotechnology companies, and in its geographic area of operations. It also took
into account the decision-making responsibilities, experience, work performance
and the prior base salaries of its executives. The Committee determined from
this review that the current base salaries of its executives fall within the
acceptable range of its base salary targets.

    ANNUAL INCENTIVE BONUS.  The compensation policy of the Company is that a
significant part of the annual compensation of each executive will be related to
and contingent upon the overall performance of the Company, the performance of
the subsidiaries or divisions for which the executive is responsible, and
individual objectives established by the executive with the CEO at the beginning
of the year. These bonus targets range from 30% to 45% of base salary. The
Committee reviewed competitive data and determined that these bonuses were
slightly higher than the average for the market-competitive set, but were
reasonable and consistent with the philosophy of having a significant portion of
executive compensation contingent on performance.

    LONG-TERM INCENTIVES.  The "1998 Long-Term Incentive Plan" that was
recommended by the Committee and approved by shareholders provides equity-based
incentive awards designed to attract and retain executives who can make
significant contributions to the Company's success, reward executives for such
significant contributions, and give executives a longer-term incentive to
increase shareholder value. Pursuant to this plan, the Committee has the
authority to grant a variety of long-term incentive awards based on the Common
Stock of the Company, including stock options (both incentive options and
non-qualified options), stock appreciation rights, restricted stock, dividend
equivalents, and other types of incentive awards. Under the plan, the Committee
has full authority to determine the provisions associated with the awards and
administer the plan. The first grants under this Plan were made in April, 1999.
Employees who received the grants included all officers of the Company, certain
senior sales and administrative employees in the fresh produce segment of the
business, and certain of the administrative employees and scientists in DNA
Plant Technology Corporation. These grants were determined based on a

                                       7
<PAGE>
survey and analysis of the competition and the market in an effort to achieve a
level above the median. Approximately 400,000 options were awarded in this first
year. A proposal for option grants for the year 2000 currently is being
evaluated.

    OTHER COMPENSATION.  The Company provides executives, officers and
management with health, retirement and other benefits under plans generally
available to the Company's employees. Mr. Fenyvesi also received certain
educational and expatriate payments consistent with arrangements he had with his
prior company.

    COMPENSATION OF CHIEF EXECUTIVE OFFICER.  Mr. Jimenez became the Chief
Executive Officer of the Company on October 1, 1997. His compensation was and is
a carryover of his arrangement as Chief Operating Officer of the
agrobiotechnology division of Savia. His base salary was increased in 1999
consistent with the rate of inflation in Mexico. The bonus that Mr. Jimenez
received for 1998 was based on an average of the performance versus plan
objectives of the three operating segments of the business--Farming,
Distribution and Research and Technology. The Committee approves the
compensation of the Chief Executive Officer of the Company on an annual basis.

    BY THE MEMBERS OF THE COMPENSATION COMMITTEE.

    Evelyn Berezin (Chairman) and Dr. Christopher Somerville.

                                       8
<PAGE>
PERFORMANCE GRAPH

    The following graph reflects the total return, which assumes reinvestment of
dividends, of a $100 investment in the Company, the Standard & Poor's 500 Stock
Index, and a competitor group index on September 27, 1996, the date on which the
Company's Common Stock first traded on the Nasdaq National Market. On
November 4, 1999 Bionova Holding Corporation's common stock moved from the
Nasdaq National Market to the American Stock Exchange.

EDGAR REPRESENTATION OF DATA POINTS USED IN PRINTED GRAPHIC

<TABLE>
<CAPTION>
          BIONOVA HOLDING CORP.  PEER GROUP INDEX  S&P 500 INDEX
<S>       <C>                    <C>               <C>
9/27/96                  100.00            100.00         100.00
12/31/96                  50.00             91.97         108.34
12/31/97                  69.42            115.87         144.48
12/31/98                  50.00             78.61         185.77
12/31/99                  21.43             42.39         224.86
</TABLE>

------------------------

1   The Peer Group is made up of the following companies: Chiquita Brands
    International, Inc., Cyanotech Corp., Dole Food Company, Inc., Fresh Del
    Monte Produce and Northland Cranberries A. Total return calculations were
    weighted according to each company's market capitalization.

                                       9
<PAGE>
ITEM 12. SECURITY OWNERSHIP OF CERTAIN BENEFICIAL OWNERS AND MANAGEMENT

SECURITY OWNERSHIP OF DIRECTORS AND EXECUTIVE OFFICERS

    The table below sets forth as of March 31, 2000, the shares of Common Stock
beneficially owned by each director, each of the Named Executive Officers, and
by all directors and executive officers as a group.

<TABLE>
<CAPTION>
                                                                       AMOUNT AND NATURE OF
                                      POSITION IN THE COMPANY          BENEFICIAL OWNERSHIP   PERCENT
            NAME                       OR OTHER OFFICES HELD             OF COMMON STOCK      OF CLASS
----------------------------  ---------------------------------------  --------------------   --------
<S>                           <C>                                      <C>                    <C>
Bernardo Jimenez............  Chief Executive Officer and Director            25,950(2)          *
Jorge Fenyvesi..............  Executive Vice President                         9,800(2)          *
Arthur H. Finnel............  Executive Vice President, Treasurer and          9,475(2)          *
                              Chief Financial Officer
Dr. John R. Bedbrook........  Executive Vice President                         2,699(1)(2)       *
Omar Diaz...................  President of International Produce               8,125(2)          *
                              Holding Company
Evelyn Berezin..............  Director                                         8,626(2)(3)       *
Dr. Peter Davis.............  Director                                             0             *
Carlos Herrera..............  Director                                             0             *
Dr. Gerald D. Laubach.......  Director                                         4,700(2)          *
Eugenio Najera..............  Director                                             0             *
Alejandro Perez.............  Director                                             0             *
Dr. Eli Shlifer.............  Director                                             0             *
Dr. Christopher R.
  Somerville................  Director                                             0             *
All directors and executive
  officers of the Company as
  a group (consisting of
  13 persons)...............                                                  69,345(4)          *
</TABLE>

------------------------

*   Represents less than 1% of Common Stock outstanding on March 31, 2000.

(1) Includes 121 shares of Common Stock held by Dr. Bedbrook's wife, as to which
    shares Dr. Bedbrook disclaims beneficial ownership.

(2) Includes currently exercisable options to purchase shares of Common Stock as
    follows: Mr. Jimenez--25,950 shares; Mr. Fenyvesi--9,800 shares;
    Mr. Finnel--9,475 shares; Mr. Diaz--8,125 shares; Ms. Berezin--3,000 shares;
    and Dr. Laubach--4,700 shares.

(3) Includes 5,626 shares of Common Stock owned jointly by Ms. Berezin and her
    husband.

(4) Gives effect to the above footnotes.

    Except as noted in the footnotes above, (i) none of such shares is known by
the Company to be shares with respect to which such person has the right to
acquire beneficial ownership, and (ii) the Company believes the beneficial
holders listed above have sole voting and investment power regarding the shares
shown as being beneficially owned by them.

                                       10
<PAGE>
SECURITY OWNERSHIP OF BENEFICIAL OWNERS

    The following table sets forth as of April 25, 2000 information with respect
to the only person who was known to the Company to be the beneficial owner of
more than five percent of the outstanding shares of Common Stock.

<TABLE>
<CAPTION>
NAME AND ADDRESS                                               NUMBER OF SHARES    PERCENT
OF BENEFICIAL OWNER                                           BENEFICIALLY OWNED   OF CLASS
-------------------                                           ------------------   --------
<S>                                                           <C>                  <C>
Bionova International, Inc.(1)..............................      18,076,839         76.6%
6701 San Pablo Avenue
Oakland, California 94608
</TABLE>

------------------------

(1) Bionova International, Inc., a Delaware corporation, is a wholly-owned
    subsidiary of Bionova, S.A. de C.V., a corporation organized under the laws
    of the United Mexican States ("Bionova Mexico"). Bionova Mexico is a
    wholly-owned subsidiary of Savia, S.A. de C.V., a corporation organized
    under the laws of the United Mexican States.

ITEM 13. CERTAIN RELATIONSHIPS AND RELATED PARTY TRANSACTIONS

THE MERGER AGREEMENT AND RELATED AGREEMENTS

    The Company acquired DNA Plant Technology Corporation ("DNAP") on
September 26, 1996, pursuant to that certain Agreement and Plan of Merger dated
January 26, 1996, as amended (the "Merger Agreement"), among Savia, Bionova
Mexico, the Company, Bionova Acquisition, Inc. and DNAP. From the date of the
Merger, Bionova International, Inc. has been the owner of at least 70% of the
outstanding shares of the Company's Common Stock, and Bionova
International, Inc. currently owns 76.6% of the outstanding shares of Common
Stock. As described above under the caption "Security Ownership of Beneficial
Owners," Bionova International, Inc. is a wholly-owned subsidiary of Bionova
Mexico, which is a wholly-owned subsidiary of Savia.

    Under the terms of the Merger Agreement, during the three-year period
immediately following the Merger, Savia agreed to provide when requested by the
Company a guarantee of the Company's indebtedness to a financial institution
under a loan or line of credit, provided that (i) Savia's maximum exposure under
such guarantee is limited to $20 million and (ii) the documents evidencing such
loan or line of credit provide that the aggregate amount loaned to the Company
thereunder will not exceed at any time the sum of (x) 80% of the accounts
receivable of the Company and its consolidated subsidiaries and (y) 50% of the
inventories of the Company and its consolidated subsidiaries and such loan is
secured by such accounts receivable and inventories. This agreement expired on
September 26, 1999.

    As provided in the Merger Agreement, Savia and DNAP entered into that
certain Long Term Funded Research Agreement dated September 26, 1996, which
provides that Savia, directly or through its affiliates, and DNAP will use their
best efforts to agree on research projects to be conducted by DNAP for Savia or
its affiliates which will result in payments to DNAP of $30 million over a
ten-year period, with minimum funding (subject to carry forwards) of $9 million
in any three-year period. Unless otherwise agreed by the parties, payments of at
least $625,000 in respect of Savia's obligation to fund research projects are to
be paid to DNAP at the beginning of each calendar quarter during the term of the
Long Term Funded Research Agreement. Effective January 1, 1997, DNAP and Seminis
Vegetable Seeds, Inc. ("SVSI"), a subsidiary of Savia, entered into a Long-Term
Research Agreement pursuant to which DNAP provides research services to SVSI,
which satisfies the minimum research commitments under DNAP's agreement with
Savia. During 1999, SVSI paid DNAP $2,500,000 with respect to work under this
agreement. In addition, DNAP earned revenue of $1,500,000 during 1999 in
accordance with the minimum funding required over the first three year period of
this long-term funded research agreement.

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<PAGE>
FINANCING

    On March 22, 1999, the Company refinanced its $85 million in consolidated
debt. This refinancing culminated in a three year $100 million credit facility
which was fully guaranteed by Savia. During 1999, the Company incurred expense
of $866,400 under this guarantee arrangement.

    On April 13, 2000, the entire amount of the Company's $100 million of Senior
Guaranteed Floating Rate Notes, due March 2002, was retired. Financing for this
early retirement of the notes was provided by Savia. Savia agreed to provide the
necessary financing to the Company on terms no less favorable than the terms of
the Floating Rate Notes. Savia also has agreed that Bionova Holding may defer
all interest payments until the final maturity date of March 23, 2002, and that
Bionova Holding will not be required to maintain any funds in an interest
reserve account.

    In addition, Savia is guaranteeing the aggregate principal amount of the
Company's short-term indebtedness. The Company is paying Savia a fee of 1.5% for
the guarantee on this short-term debt. During 1999, the Company incurred expense
of $324,000 under this guarantee arrangement. This arrangement is expected to
continue in 2000.

OTHER TRANSACTIONS WITH SAVIA AND ITS AFFILIATES

    On July 1, 1996, the Company and Bionova Mexico entered into an
Administrative Services Agreement. This agreement provides that Bionova Mexico
will render certain administrative and clerical services to the Company and its
subsidiaries in return for payment equivalent to the compensation, benefits, and
other overhead attributable to the employees of Bionova Mexico performing these
services, all of which will be performed in Mexico. The initial term of the
agreement was extended to December 31, 1996 and will continue thereafter for
successive one-year terms unless either the Company or Bionova Mexico elects to
terminate the agreement. In 1999, the amount billed by Bionova Mexico under this
agreement was $5,415,000.

    Prior to the date of the Administrative Services Agreement, Bionova Mexico
rendered certain administrative and clerical services to the Company's
subsidiaries for which certain of the Company's subsidiaries were indebted to
Bionova Mexico in the amount $4,530,000 at December 31, 1999.

    The Company contracts for insurance and factoring services with a company
that is an affiliate of Savia. During 1999, the Company incurred insurance
expense of $346,000 to this company. No amounts were due under the factoring
arrangement as of December 31, 1999. During 1999, the Company incurred interest
expense of $14,000 in connection with the factoring arrangement.

    Savia makes available to its affiliates a long-term credit line that bears
interest at variable rates comparable to those prevailing in the marketplace. At
December 31, 1999, the Company owed Savia $1,556,000 under this credit line.

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                                   SIGNATURES

    Pursuant to the requirements of Section 13 or 15(d) of the Securities
Exchange Act of 1934, the registrant has duly caused this report to be signed on
its behalf by the undersigned thereunto duly authorized.

<TABLE>
<S>                                                    <C>  <C>
                                                       BIONOVA HOLDING CORPORATION

Date: April 28, 2000                                   By:  /S/ ARTHUR H. FINNEL
                                                            -----------------------------------------
                                                            Arthur H. Finnel,
                                                            EXECUTIVE VICE PRESIDENT AND
                                                            CHIEF FINANCIAL OFFICER
</TABLE>

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