**Exhibit31.2**

**CERTIFICATIONOF PRINCIPAL FINANCIAL OFFICER**

I, John D. Prunty,certify that:

1. I have reviewed this quarterly report on Form 10-Q of OptimerPharmaceuticals, Inc.;

2. Based on my knowledge, this report does not contain any untruestatement of a material fact or omit to state a material fact necessary to makethe statements made, in light of the circumstances under which such statementswere made, not misleading with respect to the period covered by this report;

3. Based on my knowledge, the financial statements, and other financialinformation included in this report, fairly present in all material respectsthe financial condition, results of operations and cash flows of the registrantas of, and for, the periods presented in this report;

4. The registrant’s other certifying officer and I are responsible forestablishing and maintaining disclosure controls and procedures (as defined inExchange Act Rules 13a-15(e) and 15d-15(e)) for the registrant and have:

a)    designed such disclosure controls andprocedures, or caused such disclosure controls and procedures to be designedunder our supervision, to ensure that material information relating to theregistrant, including any consolidated subsidiaries, is made known to us byothers within those entities, particularly during the period in which thisreport is being prepared;

b)    evaluated the effectiveness of theregistrant’s disclosure controls and procedures and presented in this reportour conclusions about the effectiveness of the disclosure controls andprocedures, as of the end of the period covered by this report based on suchevaluation; and

c)    disclosed in this report any change in theregistrant’s internal control over financial reporting that occurred during theregistrant’s most recent fiscal quarter (the registrant’s fourth fiscal quarterin the case of an annual report) that has materially affected, or is reasonablylikely to materially affect, the registrant’s internal control over financialreporting; and

5. The registrant’s other certifying officer and I have disclosed,based on our most recent evaluation of internal control over financialreporting, to the registrant’s auditors and the audit committee of theregistrant’s board of directors (or persons performing the equivalentfunctions):

a)    all significant deficiencies and materialweaknesses in the design or operation of internal control over financialreporting which are reasonably likely to adversely affect the registrant’sability to record, process, summarize and report financial information; and

b)    any fraud, whether or not material, thatinvolves management or other employees who have a significant role in theregistrant’s internal control over financial reporting.
| Date: August 10, 2007                                                                     |
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| /s/ John D.  Prunty                                                                       |   |
| John D. Prunty                                                                            |
| Vice-President  and Chief Financial Officer  (Principal Financial and Accounting Officer) |

 

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