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                                                                     EXHIBIT 5.1


                        [COOLEY GODWARD LLP LETTERHEAD]


February 6, 2001


AURORA BIOSCIENCES CORPORATION
11010 Torreyana Road
San Diego, CA 92121

Ladies and Gentlemen:

You have requested our opinion with respect to certain matters in connection
with the filing by AURORA BIOSCIENCES CORPORATION, a Delaware corporation (the
"Company"), of a Registration Statement on Form S-4 (the "Registration
Statement") with the Securities and Exchange Commission, including a related
prospectus/proxy statement filed with the Registration Statement (the
"Prospectus"), covering the registration of 1,900,000 shares of Common Stock of
the Company (the "Shares"), proposed to be issued in connection with the merger
between PanVera Corporation, a Wisconsin corporation ("PanVera"), and Aurora
Acquisition Corp., a Wisconsin corporation and a wholly owned subsidiary of the
Company ("Merger Sub"), pursuant to the Agreement and Plan of Merger and
Reorganization dated as of November 16, 2000 (the "Merger Agreement"), among the
Company, Merger Sub and PanVera.

In connection with this opinion, we have examined the Registration Statement and
related Prospectus, the Company's Restated Certificate of Incorporation and
Bylaws, as amended, the Merger Agreement, and such other records, documents,
certificates, memoranda and other instruments as we deem necessary as a basis
for this opinion. We have assumed the genuineness and authenticity of all
documents submitted to us as originals, the conformity to originals of all
documents submitted to us as copies thereof and the due execution and delivery
of all documents where due execution and delivery are a prerequisite to the
effectiveness thereof.

On the basis of the foregoing, and in reliance thereon, we are of the opinion
that the Shares, when issued in accordance with the terms and conditions of the
Merger Agreement, will be validly issued, fully paid and nonassessable.



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Aurora Biosciences Corporation
February 6, 2001
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We consent to the reference to our firm under the caption "Legal Matters" in the
Prospectus included in the Registration Statement and to the filing of this
opinion as an exhibit to the Registration Statement.

Very truly yours,

Cooley Godward LLP


/s/ D. BRADLEY PECK
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D. Bradley Peck