EXHIBIT 5.1

                         [Cooley Godward LLP Letterhead]

May 1, 2002

Lynx Therapeutics, Inc.
25861 Industrial Blvd.
Hayward, CA 94545

Ladies and Gentlemen:

You have requested our opinion with respect to certain matters in connection
with the filing by Lynx Therapeutics, Inc., a Delaware corporation (the
"Company"), of a Registration Statement on Form S-3 (the "Registration
Statement") with the Securities and Exchange Commission covering the offering
for resale of (i) 14,600,00 shares of the Company's common stock (the "Shares"),
with a par value of $0.01, issued in connection with the Securities Purchase
Agreement, dated as of April 16, 2002, by and between the Company and the
investors named therein (the "Purchase Agreement"), (ii) up to 5,840,000 shares
of the Company's common stock (the "Investor Warrant Shares") issuable upon the
exercise of warrants for the purchase of the Company's common stock (the
"Investor Warrants"), issued in connection with the Purchase Agreement and (iii)
up to 292,000 shares of the Company's common stock (the "FBR Warrant
Shares")(collectively with the "Investor Warrant Shares", the "Warrant Shares")
issuable upon exercise of the warrant for the purchase of the Company's common
stock (the "FBR Warrant")(collectively with the "Investor Warrants", the
"Warrants"), issued in connection with the Engagement Letter, dated November 9,
2001, by and between the Company and Friedman, Billings, Ramsey & Co., Inc.
("FBR").

In connection with this opinion, we have examined the Registration Statement,
the Company's Amended and Restated Certificate of Incorporation and Bylaws, as
amended, the resolutions adopted by the Board of Directors of the Company on
April 16, 2002, and such other documents, records, 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. We have
relied upon an officer's certificate confirming receipt of payment for the
Shares upon their original issuance.

On the basis of the foregoing, and in reliance thereon, we are of the opinion
that the Shares have been validly issued, and are fully paid and nonassessable,
and the Warrant Shares, when issued upon exercise of the Warrants and payment
therefor in accordance with the terms of the Warrants, will be validly issued,
fully paid and nonassessable.

We consent to the filing of this opinion as an exhibit to the Registration
Statement and to the reference to our firm under the caption "Legal Matters" in
the Prospectus included in the Registration Statement.


Sincerely,

COOLEY GODWARD LLP


By:   /s/ James C. Kitch
      ------------------------------
      James C. Kitch