<PAGE>


   As filed with the Securities and Exchange Commission on September 14, 2000
                                                      Registration No. _________
================================================================================

                       SECURITIES AND EXCHANGE COMMISSION
                             WASHINGTON, D.C. 20549

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

                                    FORM S-8
                             REGISTRATION STATEMENT
                                      UNDER
                           THE SECURITIES ACT OF 1933

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

                                 JNI CORPORATION
             (Exact name of registrant as specified in its charter)

                  DELAWARE                              33-0740004
       (State or other jurisdiction                  (I.R.S. Employer
     of incorporation or organization)              Identification No.)

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

                             9775 TOWNE CENTRE DRIVE
                               SAN DIEGO, CA 92121
                                 (858) 535-3121
        (Address of principal executive offices, including zip code, and
                                telephone number)

                      2000 NON-QUALIFIED STOCK OPTION PLAN
                            (Full title of the plans)

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

                TERRY M. FLANAGAN                            Copies to:
        PRESIDENT AND CHIEF EXECUTIVE OFFICER         ROBERT E. BURWELL, ESQ.
                  JNI CORPORATION                         LATHAM & WATKINS
              9775 TOWNE CENTRE DRIVE               701 "B" STREET, SUITE 2100
             SAN DIEGO, CALIFORNIA 92121            SAN DIEGO, CALIFORNIA 92101
                   (858) 535-3121                         (619) 236-1234
  (Name, address, including zip code, and
telephone number, including area code, of agent
                for service)

<TABLE>
<CAPTION>

                                               CALCULATION OF REGISTRATION FEE
==========================================================================================================================
                                            Amount           Proposed Maximum     Proposed Maximum          Amount of
             Title of Securities             to be            Offering Price     Aggregate Offering       Registration
              To be Registered            Registered             Per Share              Price                  Fee
--------------------------------------------------------------------------------------------------------------------------
<S>                                    <C>               <C>                     <C>                      <C>
Common Stock, $.001 par value          1,400,000 (1)(2)          $ (3)             $96,012,618 (3)            $25,348
==========================================================================================================================
</TABLE>

(1) A maximum of 1,400,000 shares of Common Stock were reserved for issuance
    under the 2000 Non-Qualified Stock Option Plan of JNI Corporation (the
    "2000 Plan"), all of which are being registered hereunder.
(2) Pursuant to Rule 416(a), this Registration Statement shall also cover any
    additional shares of Common Stock that become issuable under the 2000 Plan
    by reason of any stock dividend, stock split, recapitalization or other
    similar transaction effected without receipt of consideration that increases
    the number of the Company's outstanding shares of Common Stock.
(3) This estimate is made pursuant to Rule 457(h) solely for purposes of
    calculating the registration fee, and is determined according to the
    following offering price information: Of the 1,400,000 shares of Common
    Stock reserved for issuance under the 2000 Plan being registered hereunder,
    (i) 258,000 shares of Common Stock are subject to outstanding options with
    an exercise price of $62.5625 per share, (ii) 24,750 shares of Common Stock
    are subject to outstanding options with an exercise price of $63.00 per
    share, and (iii) 1,117,250 shares of Common Stock are reserved for issuance
    upon exercise of options to be granted in the future. Pursuant to
    Rule 457(h), for the 1,117,250 shares of Common Stock being registered
    hereunder with an exercise price which cannot be presently determined,
    the Proposed Maximum Offering Price Per Share is $70.09375 per share of
    Common Stock, which is based on the average of the high and low prices for
    the Common Stock as reported on The Nasdaq National Market on
    September 7, 2000.

================================================================================
<PAGE>


                                     PART I

ITEM 1.  PLAN INFORMATION.

         Not required to be filed with this Registration Statement.

ITEM 2.  REGISTRANT INFORMATION AND EMPLOYEE PLAN ANNUAL INFORMATION.

         Not required to be filed with this Registration Statement.


                                     PART II

ITEM 3.  INCORPORATION OF DOCUMENTS BY REFERENCE.

         The following documents previously filed with the Securities and
Exchange Commission (the "Commission") by JNI Corporation, a Delaware
corporation (the "Company"), are hereby incorporated by reference in this
Registration Statement:

         (a)      The Annual Report on Form 10-K for the year ended December 31,
                  1999 filed March 29, 2000.

         (b)      The Quarterly Report on Form 10-Q for the quarter ended March
                  31, 2000 filed May 12, 2000.

         (c)      The Quarterly Report on Form 10-Q for the quarter ended June
                  30, 2000 filed August 14, 2000.

         (d)      The Current Report on Form 8-K filed on August 4, 2000.

         (e)      The description of the Company's Common Stock contained in the
                  Company's Registration Statement on Form 8-A filed on October
                  21, 1999.

         All documents filed by the Company pursuant to Section 13(a), 13(c), 14
or 15(d) of the Exchange Act subsequent to the date this Registration Statement
is filed with the Commission and prior to the filing of a post-effective
amendment which indicates that all securities offered have been sold or which
deregisters all securities then remaining unsold shall be deemed to be
incorporated by reference in this Registration Statement and to be a part of it
from the respective dates of filing of such documents. Any statement contained
in a document incorporated or deemed to be incorporated by reference herein
shall be deemed to be modified or superseded for purposes of this Registration
Statement to the extent that a statement contained herein or in any other
subsequently filed document which also is or is deemed to be incorporated by
reference herein modifies or supersedes such statement. Any such statement so
modified or superseded shall not be deemed, except as so modified or superseded,
to constitute a part of this Registration Statement.


<PAGE>


ITEM 4.  DESCRIPTION OF SECURITIES.

         Not applicable.

ITEM 5.  INTERESTS OF NAMED EXPERTS AND COUNSEL.

         Not applicable.

ITEM 6.  INDEMNIFICATION OF DIRECTORS AND OFFICERS.

         Section 145 of the DGCL permits indemnification of officers, directors,
and other corporate agents under certain circumstances and subject to certain
limitations. The Company's certificate of incorporation and by-laws provide that
the Company shall indemnify its directors, officers, employees and agents to the
full extent permitted by the DGCL, including circumstances in which
indemnification is otherwise discretionary under Delaware law. In addition, the
Company has entered into separate indemnification agreements with its directors
and executive officers which require the Company, among other things, to
indemnify them against certain liabilities which may arise by reason of their
status or service (other than liabilities arising from acts or omissions not in
good faith or willful misconduct).

         These indemnification provisions and the indemnification agreements
entered into between the Company and its executive officers and directors may be
sufficiently broad to permit indemnification of the Company's executive officers
and directors for liabilities, including reimbursement of expenses incurred,
arising under the Securities Act.

ITEM 7.  EXEMPTION FROM REGISTRATION CLAIMED.

         Not applicable.

ITEM 8.  EXHIBITS.

         The Exhibit Index immediately preceding the exhibits is incorporated
herein by reference.

ITEM 9.  UNDERTAKINGS.

         (a)      The undersigned Company hereby undertakes:

                  (1)      To file, during any period in which offers or sales
are being made, a post-effective amendment to this Registration Statement;

                           (i)      To include any prospectus required by
         Section 10(a)(3) of the Securities Act;

                           (ii) To reflect in the prospectus any facts or events
         arising after the effective date of this Registration Statement (or the
         most recent post-effective amendment thereof) which, individually or in
         the aggregate, represent a fundamental change in the information set
         forth in this Registration Statement. Notwithstanding the foregoing,
         any increase or decrease in volume of securities offered (if the total
         dollar


<PAGE>


         value of securities offered would not exceed that which was registered)
         and any deviation from the low or high end of the estimated maximum
         offering range may be reflected in the form of prospectus filed with
         the Commission pursuant to Rule 424(b) if, in the aggregate, the
         changes in volume and price represent no more than 20 percent change in
         the maximum aggregate offering price set forth in the "Calculation of
         Registration Fee" table in the effective Registration Statement;

                           (iii) To include any material information with
         respect to the plan of distribution not previously disclosed in this
         Registration Statement or any material change to such information in
         this Registration Statement;

PROVIDED, HOWEVER, that the undertakings set forth in paragraphs (a)(1)(i) and
(a)(1)(ii) above do not apply if the Registration Statement is on Form S-3, Form
S-8 or Form F-3, and the information required to be included in a post-effective
amendment by those paragraphs is contained in periodic reports filed with or
furnished to the Commission by the Company pursuant to Section 13 or 15(d) of
the Exchange Act that are incorporated by reference in this Registration
Statement.

                  (2) That, for the purpose of determining any liability under
the Securities Act, each such post-effective amendment shall be deemed to be a
new registration statement relating to the securities offered therein, and the
offering of such securities at that time shall be deemed to be the initial bona
fide offering thereof.

                  (3) To remove from registration by means of a post-effective
amendment any of the securities being registered which remain unsold at the
termination of the offering.

         (b) The undersigned Company hereby undertakes that, for purposes of
determining any liability under the Securities Act, each filing of the Company's
annual report pursuant to Section 13(a) or 15(d) of the Exchange Act (and, where
applicable, each filing of an employee benefit plan's annual report pursuant to
Section 15(d) of the Exchange Act) that is incorporated by reference in this
Registration Statement shall be deemed to be a new registration statement
relating to the securities offered therein, and the offering of such securities
at that time shall be deemed to be the INITIAL BONA FIDE offering thereof.

         (c) Insofar as indemnification for liabilities arising under the
Securities Act may be permitted to directors, officers and controlling persons
of the Company pursuant to the foregoing provisions, or otherwise, the Company
has been advised that in the opinion of the Commission such indemnification is
against public policy as expressed in the Securities Act and is, therefore,
unenforceable. In the event that a claim for indemnification against such
liabilities (other than the payment by the Company of expenses incurred or paid
by a director, officer or controlling person of the Company in the successful
defense of any action, suit or proceeding) is asserted by such director, officer
or controlling person in connection with the securities being registered, the
Company will, unless in the opinion of its counsel the matter has been settled
by controlling precedent, submit to a court of appropriate jurisdiction the
question whether such indemnification by it is against public policy as
expressed in the Securities Act and will be governed by the final adjudication
of such issue.


<PAGE>


                                   SIGNATURES

         Pursuant to the requirements of the Securities Act, the Company
certifies that it has reasonable grounds to believe that it meets all of the
requirements for filing on Form S-8 and has duly caused this Registration
Statement to be signed on its behalf by the undersigned, thereunto duly
authorized, in the City of San Diego, State of California, on September 13,
2000.

                            JNI Corporation

                            By: /s/ TERRY M. FLANAGAN
                               -------------------------------------------------
                                 Terry M. Flanagan
                                 President, Chief Executive Officer and Director

                                POWER OF ATTORNEY

         KNOW ALL MEN BY THESE PRESENTS, that each person whose signature
appears below hereby constitutes and appoints Terry M. Flanagan his true and
lawful attorney-in-fact, acting alone, with full power of substitution and
resubstitution for him and in his name, place and stead, in any and all
capacities to sign any and all amendments including post-effective amendments
and any registration statement filed pursuant to Rule 462(b) under the
Securities Act to this registration statement, and to file the same, with all
exhibits thereto, and other documents in connection therewith, with the
Commission, hereby ratifying and confirming all that said attorney-in-fact or
his substitute, may lawfully do or cause to be done by virtue hereof.

         Pursuant to the requirements of the Securities Act, this Registration
Statement has been signed by the following persons in the capacities and on the
dates indicated.

<TABLE>
<CAPTION>

Signature                                                       Title                                Date
---------                                                       -----                                ----
<S>                                              <C>                                         <C>
         /s/ TERRY M. FLANAGAN                   President, Chief Executive Officer and      September 13, 2000
-----------------------------------------        Director (Principal Executive Officer)
         Terry M. Flanagan

         /s/ GLORIA PURDY                        Chief Financial Officer (Principal          September 13, 2000
-----------------------------------------        Financial and Accounting Officer)
         Gloria Purdy

         /s/ ERIC P WENAAS                       Chairman of the Board of Directors          September 13, 2000
----------------------------------------
         Eric P. Wenaas

                                                 Director                                    September   , 2000
----------------------------------------
         John Bolger

                                                 Director                                    September   , 2000
----------------------------------------
         Lawrence E. Fox

         /s/ JOHN STISKA                         Director                                    September 13, 2000
----------------------------------------
         John Stiska

</TABLE>


<PAGE>


                                  EXHIBIT INDEX

<TABLE>
<CAPTION>

EXHIBIT
-------
<S>              <C>
4.1              2000 Non-Qualified Stock Option Plan of JNI Corporation,
                 terms of Sock Option Agreement and form of Stock Option
                 Grant Agreement thereunder.

5.1              Opinion of Latham & Watkins.

23.1             Consent of PricewaterhouseCoopers LLP.

23.2             Consent of Latham & Watkins (included in Exhibit 5.1 hereto).

24.1             Power of Attorney (included on signature page hereto).

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