Pacific Biosciences of California (PACB) 8-K Pacific Biosciences of California, Inc. Announces Pricing of Public Offering of Common Stock

Exhibit 5.1

650 Page Mill Road Palo Alto, CA 94304-1050   PHONE 650.493.9300 FAX 650.493.6811   www.wsgr.com

September 14, 2018

Pacific Biosciences of California, Inc.

1305 O’Brien Drive

Menlo Park, CA 94025

Ladies and Gentlemen:

We have acted as counsel to Pacific Biosciences of California, Inc., a Delaware corporation (the “Company”), in connection with the filing by the Company with the Securities and Exchange Commission (the “Commission”) of a Registration Statement on FormS-3 (Registration No. 333-219642), as amended (the “Registration Statement”), under the Securities Act of 1933, as amended (the “Act”), and declared effective on August 18, 2017. Pursuant to the Registration Statement, the Company has issued and sold 16,235,294 shares of its common stock $0.001 par value per share (the “Shares”) pursuant to that certain underwriting agreement, dated September 11, 2018 (the “Underwriting Agreement”), by and among the Company, Cowen and Company, LLC and Cantor Fitzgerald & Co., as representatives of the several underwriters named in Schedule A thereto.

We have examined the Registration Statement, together with the documents incorporated by reference therein; the related prospectus, dated August 18, 2017, filed with the Registration Statement (the “Base Prospectus”); the preliminary prospectus supplement, dated September 10, 2018, in the form filed with the Commission pursuant to Rule 424(b) of the Act relating to the offering of the Shares; and the final prospectus supplement, dated September 11, 2018, in the form filed with the Commission pursuant to Rule 424(b) of the Act relating to the offering of the Shares (together with the Base Prospectus, the “Prospectus”). In addition, we have examined originals or copies, certified or otherwise identified to our satisfaction, of such other instruments, documents, certificates and records which we have deemed relevant and necessary for the basis of our opinion hereinafter expressed. In such examination, we have assumed: (i) the authenticity of original documents and the genuineness of all signatures; (ii) the conformity to the originals of all documents submitted to us as copies; (iii) the truth, accuracy and completeness of the information, representations and warranties contained in the instruments, documents, certificates and records we have reviewed; (iv) the Underwriting Agreement has been duly authorized and validly executed and delivered by the parties thereto (other than the Company); (v) that the Shares will be issued and sold in compliance with applicable U.S. federal and state securities laws and in the manner stated in the Registration Statement and the Prospectus; and (vi) the legal capacity of all natural persons. As to any facts material to the opinions expressed herein that were not independently established or verified, we have relied upon oral or written statements and representations of officers and other representatives of the Company.

AUSTIN        BEIJING        BOSTON         BRUSSELS        HONGKONG        LONDON        LOSANGELES        NEWYORK        PALOALTO

SANDIEGO        SANFRANCISCO        SEATTLE        SHANGHAI        WASHINGTON,DC        WILMINGTON,DE

Pacific Biosciences of California, Inc.

September 14, 2018

Page 2 of 2

We express no opinion herein as to the laws of any state or jurisdiction other than the General Corporation Law of the State of Delaware (including the statutory provisions and all applicable judicial decisions interpreting those laws) and the federal laws of the United States of America.

We express no opinion as to (i) the effect of any bankruptcy, insolvency, reorganization, arrangement, fraudulent conveyance, moratorium or other similar laws relating to or affecting the rights of creditors generally, (ii) rights to indemnification and contribution which may be limited by applicable law or equitable principles, or (iii) the effect of general principles of equity, including, without limitation, concepts of materiality, reasonableness, good faith and fair dealing, the effect of judicial discretion and the possible unavailability of specific performance, injunctive relief or other equitable relief, and the limitations on rights of acceleration, whether considered in a proceeding in equity or at law.

On the basis of the foregoing, we are of the opinion that the Shares, when issued, delivered and paid for in accordance with the terms of the Underwriting Agreement, will be validly issued, fully paid andnon-assessable.

We hereby consent to the filing of this opinion as an exhibit to the Current Report on Form8-K dated as of the date hereof filed by the Company and incorporated by reference into the Registration Statement and to the use of our name wherever it appears in the Registration Statement, the Prospectus and in any amendment or supplement thereto. In giving such consent, we do not believe that we are “experts” within the meaning of such term as used in the Act or the rules and regulations of the Securities and Exchange Commission issued thereunder with respect to any part of the Registration Statement, including this opinion as an exhibit or otherwise.

Very truly yours,

/s/ Wilson Sonsini Goodrich & Rosati

WILSON SONSINI GOODRICH & ROSATI

Professional Corporation