**Exhibit31.2**

**CERTIFICATIONOF PRINCIPAL FINANCIAL OFFICER**

I, John D. Prunty,certify that:

1. I have reviewed thisquarterly report on Form 10-Q of Optimer Pharmaceuticals, Inc.;

2. Based on my knowledge,this report does not contain any untrue statement of a material fact or omit tostate a material fact necessary to make the statements made, in light of thecircumstances under which such statements were made, not misleading withrespect to the period covered by this report;

3. Based on my knowledge,the financial statements, and other financial information included in thisreport, fairly present in all material respects the financial condition,results of operations and cash flows of the registrant as of, and for, theperiods presented in this report;

4. The registrant’s othercertifying officer and I are responsible for establishing and maintainingdisclosure controls and procedures (as defined in Exchange ActRules 13a-15(e) and 15d-15(e)) for the registrant and have:

a)              designedsuch disclosure controls and procedures, or caused such disclosure controls andprocedures to be designed under our supervision, to ensure that materialinformation relating to the registrant, including any consolidatedsubsidiaries, is made known to us by others within those entities, particularlyduring the period in which this report is being prepared;

b)             evaluatedthe effectiveness of the registrant’s disclosure controls and procedures andpresented in this report our conclusions about the effectiveness of thedisclosure controls and procedures, as of the end of the period covered by thisreport based on such evaluation; and

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

5. The registrant’s othercertifying officer and I have disclosed, based on our most recent evaluation ofinternal control over financial reporting, to the registrant’s auditors and theaudit committee of the registrant’s board of directors (or persons performingthe equivalent functions):

a)              all significantdeficiencies and material weaknesses in the design or operation of internalcontrol over financial reporting which are reasonably likely to adverselyaffect the registrant’s ability to record, process, summarize and reportfinancial information; and

b)             anyfraud, whether or not material, that involves management or other employees whohave a significant role in the registrant’s internal control over financialreporting.
| Date: May 10, 2007                            |   |   |
|-----------------------------------------------|--------|--------|
|                                          |   |   |
| /s/ John D. Prunty                            |   |   |   |
| John D. Prunty                                |   |   |
| Vice-President  and Chief Financial Officer   |   |   |
| (Principal  Financial and Accounting Officer) |   |   |
|                                               |        |        |  |

 

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