|   |
|---|
|   |  |
| x | ANNUAL REPORT PURSUANT TO SECTION 13 OR 15(d) OF THE SECURITIES EXCHANGE ACT OF 1934 |

|   |
|---|
|   |  |
| o | TRANSITION REPORT PURSUANT TO SECTION 13 OR 15(D) OF THE SECURITIES EXCHANGE ACT OF 1934 |

|                                 |
|---------------------------------|
|                                 |  |  |
| Delaware                        |   | 68-0533693 |
| (State or other jurisdiction of |   | (I.R.S. Employer |
| incorporation or organization)  |   | Identification No.) |

|                                |
|--------------------------------|
|                                |  |  |
| Title of each class            |   | Name of each exchange on which registered |
| Common Stock, $0.001 par value |   | The NASDAQ Global Market |

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|                                               |
|-----------------------------------------------|
|                                               |  |  |
| Large accelerated Filer o                     |   | Accelerated Filer o |
|                                          |   |   |
| Non-accelerated Filer x                       |   | Smaller Reporting Company o |
|                                          |   |   |
| (Do not check if a smaller reporting company) |   |   |

----

|    |                       |
|----|-----------------------|
| 1. | Financial Statements* |

|    |                               |
|----|-------------------------------|
| 2. | Financial Statement Schedules |

|    |          |
|----|----------|
| 3. | Exhibits |

----

|                           |
|---------------------------|
|                           |  |  |
| Date: April 13, 2015 | ACHAOGEN, INC. |
|                      | By: | /s/ Derek A. Bertocci  |
|                      |   | Derek A. Bertocci |
|                      |   | Senior Vice President and Chief Financial Officer(Principal Financial and Accounting Officer) |

----

|                |
|----------------|
|                |  |  |  |  |  |  |  |  |  |  |  |  |
|           |   |   |   | Incorporated by Reference from |   | Provided Herewith |
| Exhibit Number |   | Description of Document |   | Registrant's Form |   | File No. |   | Date Filed with the SEC |   | Exhibit Number |   |   |
|           |   |   |   |   |   |   |   |   |   |   |   |   |
| 3.1            |   | Amended and Restated Certificate of Incorporation of Achaogen, Inc. |   | 8-K |   | 001-36323 |   | 3/17/2014 |   | 3.1 |   |   |
| 3.2            |   | Amended and Restated Bylaws of Achaogen, Inc. |   | 8-K |   | 001-36323 |   | 3/17/2014 |   | 3.2 |   |   |
| 4.1            |   | Form of Common Stock Certificate. |   | S-1/A |   | 333-193559 |   | 2/25/2014 |   | 4.1 |   |   |
| 4.2            |   | Warrant issued to Oxford Finance LLC on November 1, 2011. |   | S-1 |   | 333-193559 |   | 1/24/2014 |   | 4.4 |   |   |
| 4.3            |   | Warrant issued to Silicon Valley Bank on November 1, 2011. |   | S-1 |   | 333-193559 |   | 1/24/2014 |   | 4.5 |   |   |
| 4.4            |   | Warrant issued to Oxford Finance LLC on April 30, 2012 (Term A Loan (2)). |   | S-1 |   | 333-193559 |   | 1/24/2014 |   | 4.6 |   |   |
| 4.5            |   | Warrant issued to Oxford Finance LLC on April 30, 2012 (Term B Loan). |   | S-1 |   | 333-193559 |   | 1/24/2014 |   | 4.7 |   |   |
| 10.1(A)† |   | License Agreement, dated January 25, 2006, by and between the registrant and Isis Pharmaceuticals, Inc. |   | S-1/A |   | 333-193559 |   | 2/27/2014 |   | 10.5(A) |   |   |
| 10.1(B)† |   | Letter Agreement, dated January 25, 2006, by and between the registrant and Isis Pharmaceuticals, Inc. |   | S-1 |   | 333-193559 |   | 1/24/2014 |   | 10.5(B) |   |   |
| 10.2(A)† |   | Development Services Agreement, dated August 19, 2013, by and between the registrant and ARK Diagnostics, Inc. |   | S-1/A |   | 333-193559 |   | 2/27/2014 |   | 10.6 |   |   |
| 10.2(B)        |   | Amendment No. 1 dated April 1, 2014 to the Development Services Agreement dated August 19, 2013 by and between the registrant and ARK Diagnostics, Inc. |   |   |   |   |   |   |   |   |   | X |
| 10.3(A)† |   | Contract Award issued by the Biomedical Advanced Research and Development Authority of the United States Department of Health and Human Services, dated August 30, 2010. |   | S-1/A |   | 333-193559 |   | 2/27/2014 |   | 10.7(A) |   |   |
| 10.3(B)        |   | Modification 0001, dated February 24, 2011, to Contract Award issued by the Biomedical Advanced Research and Development Authority of the United States Department of Health and Human Services, dated August 30, 2010. |   | S-1 |   | 333-193559 |   | 1/24/2014 |   | 10.7(B) |   |   |
| 10.3(C)† |   | Modification 0003, dated August 18, 2011, to Contract Award issued by the Biomedical Advanced Research and Development Authority of the United States Department of Health and Human Services, dated August 30, 2010. |   | S-1 |   | 333-193559 |   | 1/24/2014 |   | 10.7(C) |   |   |
| 10.3(D)† |   | Modification 0004, dated July 16, 2012, to Contract Award issued by the Biomedical Advanced Research and Development Authority of the United States Department of Health and Human Services, dated August 30, 2010. |   | S-1 |   | 333-193559 |   | 1/24/2014 |   | 10.7(D) |   |   |
| 10.3(E)† |   | Modification 0006, dated September 20, 2012, to Contract Award issued by the Biomedical Advanced Research and Development Authority of the United States Department of Health and Human Services, dated August 30, 2010. |   | S-1 |   | 333-193559 |   | 1/24/2014 |   | 10.7(E) |   |   |

----

|                |
|----------------|
|                |  |  |  |  |  |  |  |  |  |  |  |  |
|           |   |   |   | Incorporated by Reference from |   | Provided Herewith |
| Exhibit Number |   | Description of Document |   | Registrant's Form |   | File No. |   | Date Filed with the SEC |   | Exhibit Number |   |   |
|           |   |   |   |   |   |   |   |   |   |   |   |   |
| 10.3(F)† |   | Modification 0007, dated January 23, 2013, to Contract Award issued by the Biomedical Advanced Research and Development Authority of the United States Department of Health and Human Services, dated August 30, 2010. |   | S-1 |   | 333-193559 |   | 1/24/2014 |   | 10.7(F) |   |   |
| 10.3(G)† |   | Modification 0008, dated February 28, 2013, to Contract Award issued by the Biomedical Advanced Research and Development Authority of the United States Department of Health and Human Services, dated August 30, 2010. |   | S-1 |   | 333-193559 |   | 1/24/2014 |   | 10.7(G) |   |   |
| 10.3(H)† |   | Modification 0009, dated April 22, 2013, to Contract Award issued by the Biomedical Advanced Research and Development Authority of the United States Department of Health and Human Services, dated August 30, 2010. |   | S-1 |   | 333-193559 |   | 1/24/2014 |   | 10.7(H) |   |   |
| 10.3(I)† |   | Modification 0010, dated August 14, 2013, to Contract Award issued by the Biomedical Advanced Research and Development Authority of the United States Department of Health and Human Services, dated August 30, 2010. |   | S-1 |   | 333-193559 |   | 1/24/2014 |   | 10.7(I) |   |   |
| 10.3(J)† |   | Modification 0011, dated August 30, 2013, to Contract Award issued by the Biomedical Advanced Research and Development Authority of the United States Department of Health and Human Services, dated August 30, 2010. |   | S-1 |   | 333-193559 |   | 1/24/2014 |   | 10.7(J) |   |   |
| 10.3(K)† |   | Modification 0012, dated November 5, 2013, to Contract Award issued by the Biomedical Advanced Research and Development Authority of the United States Department of Health and Human Services, dated August 30, 2010. |   | S-1 |   | 333-193559 |   | 1/24/2014 |   | 10.7(K) |   |   |
| 10.3(L)† |   | Modification 0013, dated December 17, 2013, to Contract Award issued by the Biomedical Advanced Research and Development Authority of the United States Department of Health and Human Services, dated August 30, 2010. |   | S-1 |   | 333-193559 |   | 1/24/2014 |   | 10.7(L) |   |   |
| 10.3(M)        |   | Modification 0014, dated April 14, 2014, to Contract Award issued by the Biomedical Advanced Research and Development Authority of the United States Department of Health and Human Services, dated August 30, 2010. |   |   |   |   |   |   |   |   |   | X |
| 10.3(N)        |   | Modification 0015, dated May 12, 2014, to Contract Award issued by the Biomedical Advanced Research and Development Authority of the United States Department of Health and Human Services, dated August 30, 2010. |   |   |   |   |   |   |   |   |   | X |
| 10.3(O)        |   | Modification 0016, dated July 10, 2014, to Contract Award issued by the Biomedical Advanced Research and Development Authority of the United States Department of Health and Human Services, dated August 30, 2010. |   |   |   |   |   |   |   |   |   | X |

----

|                |
|----------------|
|                |  |  |  |  |  |  |  |  |  |  |  |  |
|           |   |   |   | Incorporated by Reference from |   | Provided Herewith |
| Exhibit Number |   | Description of Document |   | Registrant's Form |   | File No. |   | Date Filed with the SEC |   | Exhibit Number |   |   |
|           |   |   |   |   |   |   |   |   |   |   |   |   |
| 10.3(P)        |   | Modification 0017, dated July 18, 2014, to Contract Award issued by the Biomedical Advanced Research and Development Authority of the United States Department of Health and Human Services, dated August 30, 2010. |   |   |   |   |   |   |   |   |   | X |
| 10.3(Q)        |   | Modification 0018, dated December 17, 2014, to Contract Award issued by the Biomedical Advanced Research and Development Authority of the United States Department of Health and Human Services, dated August 30, 2010. |   |   |   |   |   |   |   |   |   | X |
| 10.4           |   | Loan and Security Agreement, dated November 1, 2011, by and among the registrant, Oxford Finance LLC and Silicon Valley Bank. |   | S-1 |   | 333-193559 |   | 1/24/2014 |   | 10.8 |   |   |
| 10.5           |   | Third Amended and Restated Investors’ Rights Agreement, dated March 6, 2013, by and among the registrant and certain stockholders. |   | S-1 |   | 333-193559 |   | 1/24/2014 |   | 10.15 |   |   |
| 10.6(A)        |   | Amended and Restated Lease Agreement, dated December 29, 2010, by and between the registrant and ARE-San Francisco No. 17, LLC. |   | S-1 |   | 333-193559 |   | 1/24/2014 |   | 10.9(A) |   |   |
| 10.6(B)        |   | Letter Agreement, dated January 4, 2011, by and between the registrant and ARE-San Francisco No. 17, LLC. |   | S-1 |   | 333-193559 |   | 1/24/2014 |   | 10.9(B) |   |   |
| 10.6(C)        |   | Letter Agreement, dated June 15, 2011, by and between the registrant and ARE-San Francisco No. 17, LLC. |   | S-1 |   | 333-193559 |   | 1/24/2014 |   | 10.9(C) |   |   |
| 10.6(D)        |   | First Amendment, dated April 1, 2013, to that certain Amended and Restated Lease Agreement, dated December 29, 2010, by and between the registrant and ARE-San Francisco No. 17, LLC. |   | S-1 |   | 333-193559 |   | 1/24/2014 |   | 10.9(D) |   |   |
| 10.6(E)        |   | Second Amendment, dated June 28, 2013, to that certain Amended and Restated Lease Agreement, dated as of December 29, 2010, by and between the registrant and ARE-San Francisco No. 17, LLC. |   | S-1 |   | 333-193559 |   | 1/24/2014 |   | 10.9(E) |   |   |
| 10.7(A)#       |   | Achaogen, Inc. Amended and Restated 2003 Stock Plan, as amended. |   | S-8 |   | 333-195348 |   | 4/17/2014 |   | 99.1 |   |   |
| 10.7(B)#       |   |  Amendment to Amended and Restated 2003 Stock Plan, as amended. |   | 10-K |   | 001-36323 |   | 3/16/2015 |   | 10.8(B) |   |   |
| 10.7(C)#       |   |  Form of Stock Option Agreement under Achaogen, Inc. Amended and Restated 2003 Stock Plan. |   | S-1 |   | 333-193559 |   | 1/24/2014 |   | 10.1(B) |   |   |
| 10.8(A)#       |   |  Achaogen, Inc. 2014 Equity Incentive Award Plan. |   | S-8 |   | 333-195348 |   | 4/17/2014 |   | 99.3 |   |   |
| 10.8(B)#       |   |  Form of Stock Option Agreement under Achaogen, Inc. 2014 Equity Incentive Award Plan. |   | S-1/A |   | 333-193559 |   | 2/12/2014 |   | 10.2(B) |   |   |
| 10.8(C)#       |   |  Form of Restricted Stock Agreement under Achaogen, Inc. 2014 Equity Incentive Award Plan. |   | S-1/A |   | 333-193559 |   | 2/12/2014 |   | 10.2(C) |   |   |
| 10.8(D)#       |   |  Form of Restricted Stock Unit Award Grant Notice and Restricted Stock Unit Award Agreement under Achaogen, Inc. 2014 Equity Incentive Award Plan. |   | 10-K |   | 001-36323 |   | 3/16/2015 |   | 10.9(D) |   |   |

----

|                |
|----------------|
|                |  |  |  |  |  |  |  |  |  |  |  |  |
|           |   |   |   | Incorporated by Reference from |   | Provided Herewith |
| Exhibit Number |   | Description of Document |   | Registrant's Form |   | File No. |   | Date Filed with the SEC |   | Exhibit Number |   |   |
|           |   |   |   |   |   |   |   |   |   |   |   |   |
| 10.9#          |   |  Achaogen, Inc. 2014 Employee Stock Purchase Plan. |   | S-8 |   | 333-195348 |   | 4/17/2014 |   | 99.7 |   |   |
| 10.10(A)#      |   | Achaogen, Inc. 2014 Employment Commencement Incentive Plan. |   | 10-K |   | 001-36323 |   | 3/16/2015 |   | 10.11(A) |   |   |
| 10.10(B)#      |   | Form of Stock Option Grant Notice and Stock Option Agreement under the Achaogen, Inc. 2014 Employment Commencement Incentive Plan. |   | 10-K |   | 001-36323 |   | 3/16/2015 |   | 10.11(B) |   |   |
| 10.10(C)#      |   | Form of Restricted Stock Unit Award Grant Notice and Restricted Stock Unit Award Agreement under the Achaogen, Inc. 2014 Employment Commencement Incentive Plan. |   | 10-K |   | 001-36323 |   | 3/16/2015 |   | 10.11(C) |   |   |
| 10.11#         |   | Change in Control Plan. |   | S-1 |   | 333-193559 |   | 1/24/2014 |   | 10.14 |   |   |
| 10.12#         |   | Form of Indemnification Agreement between the registrant and its directors and officers. |   | S-1/A |   | 333-193559 |   | 2/12/2014 |   | 10.3 |   |   |
| 10.13#         |   | Offer Letter, dated January 24, 2011, by and between the registrant and Kenneth J. Hillan M.B., Ch.B. |   | S-1 |   | 333-193559 |   | 1/24/2014 |   | 10.10 |   |   |
| 10.14#         |   | Offer Letter, dated February 14, 2014, by and between the registrant and Derek A. Bertocci. |   | S-1/A |   | 333-193559 |   | 2/25/2014 |   | 10.17 |   |   |
| 10.15#         |   | Offer Letter, dated June 24, 2014, by and between the registrant and Ian Friedland, M.D. |   | 10-Q |   | 001-36323 |   | 8/11/2014 |   | 10.1 |   |   |
| 10.16#         |   | Offer Letter, dated May 2, 2011, by and between the registrant and Becki Filice. |   | S-1 |   | 333-193559 |   | 1/24/2014 |   | 10.11 |   |   |
| 10.17#         |   | Offer Letter, dated July 27, 2011, by and between the registrant and Christine Murray. |   | S-1 |   | 333-193559 |   | 1/24/2014 |   | 10.12 |   |   |
| 10.18#         |   | Offer Letter, dated December 29, 2012, by and between the registrant and Dennis Hom. |   | S-1 |   | 333-193559 |   | 1/24/2014 |   | 10.13 |   |   |
| 10.19#         |   | Separation Agreement, dated March 31, 2014, by and between the registrant and Dennis Hom. |   | 10-Q |   | 001-36323 |   | 5/12/2014 |   | 10.1 |   |   |
| 23.1           |   | Consent of Ernst & Young LLP, Independent Registered Public Accounting Firm. |   | 10-K |   | 001-36323 |   | 3/16/2015 |   | 23.1 |   |   |
| 31.1           |   | Certification of Principal Executive Officer Required Under Rule 13a-14(a) and 15d-14(a) of the Securities Exchange Act of 1934, as amended. |   | 10-K |   | 001-36323 |   | 3/16/2015 |   | 31.1 |   |   |
| 31.2           |   | Certification of Principal Financial Officer Required Under Rule 13a-14(a) and 15d-14(a) of the Securities Exchange Act of 1934, as amended. |   | 10-K |   | 001-36323 |   | 3/16/2015 |   | 31.2 |   |   |
| 31.3           |   | Certification of Principal Executive Officer Required Under Rule 13a-14(a) and 15d-14(a) of the Securities Exchange Act of 1934, as amended. |   |   |   |   |   |   |   |   |   | X |
| 31.4           |   | Certification of Principal Financial Officer Required Under Rule 13a-14(a) and 15d-14(a) of the Securities Exchange Act of 1934, as amended. |   |   |   |   |   |   |   |   |   | X |
| 32.1*          |   | Certification of Principal Executive Officer and Principal Financial Officer Required Under Rule 13a-14(b) of the Securities Exchange Act of 1934, as amended, and 18 U.S.C. §1350. |   | 10-K |   | 001-36323 |   | 3/16/2015 |   | 32.1 |   |   |
| 101.INS        |   | XBRL Instance Document. |   | 10-K |   | 001-36323 |   | 3/16/2015 |   | 101.INS |   |   |
| 101.SCH        |   | XBRL Taxonomy Extension Schema Document. |   | 10-K |   | 001-36323 |   | 3/16/2015 |   | 101.SCH |   |   |

----

|                |
|----------------|
|                |  |  |  |  |  |  |  |  |  |  |  |  |
|           |   |   |   | Incorporated by Reference from |   | Provided Herewith |
| Exhibit Number |   | Description of Document |   | Registrant's Form |   | File No. |   | Date Filed with the SEC |   | Exhibit Number |   |   |
|           |   |   |   |   |   |   |   |   |   |   |   |   |
| 101.CAL        |   | XBRL Taxonomy Extension Calculation Linkbase Document. |   | 10-K |   | 001-36323 |   | 3/16/2015 |   | 101.CAL |   |   |
| 101.DEF        |   | XBRL Taxonomy Extension Definition Linkbase Document. |   | 10-K |   | 001-36323 |   | 3/16/2015 |   | 101.DEF |   |   |
| 101.LAB        |   | XBRL Taxonomy Extension Label Linkbase Document. |   | 10-K |   | 001-36323 |   | 3/16/2015 |   | 101.LAB |   |   |
| 101.PRE        |   | XBRL Taxonomy Extension Presentation Linkbase Document. |   | 10-K |   | 001-36323 |   | 3/16/2015 |   | 101.PRE |   |   |

|                                                                                                                                                                                                                                                                                                                                                                                                                                                |
|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|
|                                                                                                                                                                                                                                                                                                                                                                                                                                                |
| † Confidential treatment has been granted for certain information contained in this exhibit. Such information has been omitted and filed separately with the SEC.                                                                                                                                                                                                                                                                        |
| # Indicates management contract or compensatory plan.                                                                                                                                                                                                                                                                                                                                                                                          |
| * The certification attached as Exhibit 32.1 that accompanies this Amendment No. 1 is not deemed filed with the SEC and is not to be incorporated by reference into any filing of Achaogen, Inc. under the Securities Act of 1933, as amended, or the Securities Exchange Act of 1934, as amended, whether made before or after the date of this Amendment No. 1, irrespective of any general incorporation language contained in such filing. |