Exhibit 10.1

EXCHANGE AGREEMENT

                                          (including any other persons or entities exchanging Existing Notes hereunder for whom the undersigned Holder holds contractual and investment authority, the “ Holder ”) enters into this Exchange Agreement (this “ Agreement ”) with Verenium Corporation (the “ Company ”) on August 28, 2009, whereby on the date hereof the Holder will exchange (the “ Exchange ”) the Company’s 5.50% Convertible Senior Notes due 2027 (the “ Existing Notes ”) for the Company’s new 9.00% Convertible Senior Secured Notes due 2027 (the “ New Notes ”) that will be issued pursuant to the provisions of an Indenture (the “ Indenture ”) to be entered into by and between the Company and Wells Fargo Bank, National Association, as trustee (the “ Trustee ”).

On and subject to the terms hereof, the parties hereto agree as follows:

Article I : Exchange of the Existing Notes for New Notes

At the Closing (as defined herein), the Holder hereby agrees to exchange and deliver to the Company the following Existing Notes, and in exchange therefor the Company hereby agrees to issue to the Holder the principal amount of New Notes described below and to pay in cash the following accrued but unpaid interest on such Existing Notes:

The closing of the Exchange (the “ Closing ”) shall occur no later than three business days after the date of this Agreement (assuming the timely delivery of the Exchanged Notes). At the Closing, (a) the Holder shall deliver or cause to be delivered to the Company all right, title and interest in and to the Exchanged Notes free and clear of any mortgage, lien, pledge, charge, security interest, encumbrance, title retention agreement, option, equity or other adverse claim thereto (collectively, “ Liens ”), and all documentation related thereto, and whatever documents of conveyance or transfer may be necessary or desirable to transfer to and confirm in the Company all right, title and interest in and to the Exchanged Notes free and clear of any Liens, (b) the Company shall issue to the Holder the Holder’s New Notes and (c) the Company shall deliver to the Holder the Cash Payment; provided, however, that the parties acknowledge that the issuance of the Holder’s New Notes to the Holder may be delayed due to procedures and mechanics within the system of The Depository Trust Company and that such delay will not be a default under this Agreement so long as (i) the Company is using commercially reasonable efforts to effect the issuance of one or more global notes representing the New Notes, (ii) such delay is no longer than three business days and (iii) interest shall accrue on such New Notes from the date of the Indenture. Simultaneously with or after the Closing, the Company may issue New Notes to one or more other holders of outstanding Existing Notes, subject to the terms of the Indenture.

Article II : Covenants, Representations and Warranties of the Holder

The Holder hereby covenants as follows, and makes the following representations and warranties, each of which is and shall be true and correct on the date hereof and at the Closing, to the Company, Lazard Frères & Co. LLC and Lazard Capital Markets LLC, and all such covenants, representations and warranties shall survive the Exchange.

Section 2.1 Power and Authorization .  The Holder is duly organized, validly existing and in good standing, and has the power, authority and capacity to execute and deliver this Agreement, to perform its obligations hereunder, and to consummate the Exchange contemplated hereby. If the Holder that is signatory hereto is executing this Agreement to effect the exchange of Exchanged Notes beneficially owned by one or more other persons or entities (who are thus included in the definition of “Holder” hereunder), (a) such signatory Holder has all requisite discretionary authority to enter into this Agreement on behalf of, and bind, each such other person or entity that is a beneficial owner of Exchanged Notes, and (b)  Exhibit A hereto is a true, correct and complete list of (i) the name of each party delivering (as beneficial owner) Exchanged Notes hereunder, (ii) the principal amount of such Holder’s Exchanged Notes, (iii) the principal amount of Holder’s New Notes to be issued to such Holder in respect of its Exchanged Notes, and (iv) the amount of the cash payment to be made to such Holder in respect of the accrued interest on its Exchanged Notes.

Section 2.2 Valid and Enforceable Agreement; No Violations .  This Agreement has been duly executed and delivered by the Holder and constitutes a legal, valid and binding obligation of the Holder, enforceable against the Holder in accordance with its terms, except that such enforcement may be subject to (a) bankruptcy, insolvency, reo