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| [X] | ANNUAL      REPORT PURSUANT TO SECTION 13 OR 15(D) OF THE SECURITIES EXCHANGE ACT      OF 1934 |
|-----|----------------------------------------------------------------------------------------------------------|

| ATLAS      MINING COMPANY                                                    |
|------------------------------------------------------------------------------|
| (Exact      name of registrant as specified in its charter)                  |
| Idaho                                                                        |   | 82-0096527 |
| (State      or other jurisdiction of incorporation or    organization)  |   | (I.R.S.      Employer Identification No.)  |

| 110      Greene Street – Ste 1101, New York, NY |                                                | 10012           |
|-------------------------------------------------------|-----------------------------------------------------|-----------------|
| (Address      of principal executive offices)    |                                                | (Zip      Code) |
|                                                  | (208)      556-1181                                 |            |   |
|                                                  | Issuer's      telephone number, including area code |            |   |

|   | YES |   | NO | x |
|--------|-----|--------|----|---|

Indicate by check mark if the registrant is not required to filereports pursuant to Section 13 or 15(d) of the Act:

|   | YES |   | NO | x |
|--------|-----|--------|----|---|

|   | YES |   | NO | x |
|--------|-----|--------|----|---|

|   |   |   |   |   |
|--------|--------|--------|--------|--------|

| Large      Accelerated Filer |   | Accelerated      Filer |   | Non-accelerated      Filer |   | Smaller      Reporting Company | x |
|------------------------------|--------|------------------------|--------|----------------------------|--------|--------------------------------|---|

|   | YES |   | NO | x |
|--------|-----|--------|----|---|

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| Exhibit |                                                                                                                                                                                                  |   |
|---------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|--------|
| Number  | Description      of Exhibit                                                                                                                                                                           |   |
|    |                                                                                                                                                                                                  |   |
| 31.3    | Amended      certification pursuant to Rule 13a-14 of the Securities Exchange Act, as      adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002, of the      Principal Executive Officer |   |
| 31.4    | Amended      certification pursuant to Rule 13a-14 of the Securities Exchange Act, as      adopted pursuant to Section 302 of the Sarbanes-Oxley Act of 2002, of the      Principal Financial Officer |   |

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|   |   | Applied      Minerals, Inc           |   |
|--------|--------|--------------------------------------|--------|
|   |   |                                 |   |
|   | By:    |                                 |   |
|   |   | Andre      Zeitoun                   |   |
|   |   | Chief      Executive Officer         |   |
|   |   |                                 |   |
|   | By:    |                                 |   |
|   |   | Christopher      T. Carney           |   |
|   |   | Interim      Chief Financial Officer |   |

| Signature            | Title    | Date                  |
|----------------------|----------|-----------------------|
|                 |     |                  |
|                 | Director | February      4, 2010 |
| John      F. Levy    |     |                  |
|                 |     |                  |
|                 | Director | February      4, 2010 |
| David      Taft      |     |                  |
|                 |     |                  |
|                 | Director | February      4, 2010 |
| Morris      D. Weiss |     |                  |
|                 |     |                  |
|                 | Director | February      4, 2010 |
| Andre      Zeitoun   |     |                  |
|                 |     |                  |
|                 | Director | February      4, 2010 |
| Evan      Stone      |     |                  |

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| 1.   | I      have reviewed this 10-K/A (Amendment No. 3) of Applied Minerals, Inc. for      the period ended December 31, 2008; |
|----------------|---------------------------------------------------------------------------------------------------------------------------|

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

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

| 4.   | The      registrant's other certifying officer(s) and I are responsible for      establishing and maintaining disclosure controls and procedures (as      defined in Exchange Act Rules 13a-15(e) and 15d-15(e)) and internal      control over financial reporting (as defined in Exchange Act Rules      13a-15(f) and 15d-15(f)) for the registrant and  have: |
|----------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| i.   | Designed      such disclosure controls and procedures, or caused such disclosure      controls and procedures to be designed under our supervision, to ensure      that material information relating to the registrant, including its      consolidated subsidiaries, is made known to us by others within those      entities, particularly during the period in which this report is being      prepared; |
|----------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| ii.   | Designed      such internal control over financial reporting, or caused such internal      control over financial reporting to be designed under our supervision, to      provide reasonable assurance regarding the reliability of financial      reporting and the preparation of financial statements for external      purposes in accordance with generally accepted accounting      principles; |
|-----------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| iii.   | Evaluated      the effectiveness of the registrant's disclosure controls and procedures      and presented in this report our conclusions about the effectiveness of      the disclosure controls and procedures, as of the end of the period      covered by this report based on such evaluation;  and |
|------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| iv.   | Disclosed      in this report any change in the registrant's internal control over      financial reporting that occurred during the registrant's most recent      fiscal quarter (the registrant's fourth fiscal quarter in the case of an      annual report) that has materially affected, or is reasonably likely to      materially affect, the registrant's internal control over financial      reporting; and |
|-----------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| 5.   | The      registrant's other certifying officer(s) and I have disclosed, based on      our most recent evaluation of internal control over financial reporting,      to the registrant's auditors and the audit committee of the registrant's      board of directors (or persons performing the equivalent      functions): |
|----------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| i.   | All      significant deficiencies and material weaknesses in the design or      operation of internal control over financial reporting which are      reasonably likely to adversely affect the registrant's ability to record,      process, summarize and report financial information;  and |
|----------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| ii.   | Any      fraud, whether or not material, that involves management or other      employees who have a significant role in the registrant's internal control      over financial reporting. |
|-----------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

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| 1.   | I have reviewed this 10-K/A (Amendment No. 3) of Applied      Minerals, Inc. for the period ended December 31,  2008; |
|----------------|-----------------------------------------------------------------------------------------------------------------------|

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

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

| 4.   | The registrant's other certifying officer(s) and I are      responsible for establishing and maintaining disclosure controls and      procedures (as defined in Exchange Act Rules 13a-15(e) and 15d-15(e)) and      internal control over financial reporting (as defined in Exchange Act      Rules 13a-15(f) and 15d-15(f)) for the registrant and      have: |
|----------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| i.   | Designed such disclosure controls and procedures, or caused      such disclosure controls and procedures to be designed under our      supervision, to ensure that material information relating to the      registrant, including its consolidated subsidiaries, is made known to us      by others within those entities, particularly during the period in which      this report is being prepared; |
|----------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| ii.   | Designed such internal control over financial reporting, or      caused such internal control over financial reporting to be designed under      our supervision, to provide reasonable assurance regarding the reliability      of financial reporting and the preparation of financial statements for      external purposes in accordance with generally accepted accounting      principles; |
|-----------------|--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| iii.   | Evaluated the effectiveness of the registrant's disclosure      controls and procedures and presented in this report our conclusions about      the effectiveness of the disclosure controls and procedures, as of the end      of the period covered by this report based on such evaluation;      and |
|------------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| iv.   | Disclosed in this report any change in the registrant's      internal control over financial reporting that occurred during the      registrant's most recent fiscal quarter (the registrant's fourth fiscal      quarter in the case of an annual report) that has materially affected, or      is reasonably likely to materially affect, the registrant's internal      control over financial reporting;and |
|-----------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| 5.   | The registrant's other certifying officer(s) and I have      disclosed, based on our most recent evaluation of internal control over      financial reporting, to the registrant's auditors and the audit committee      of the registrant's board of directors (or persons performing the      equivalent functions): |
|----------------|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| i.   | All significant deficiencies and material weaknesses in the      design or operation of internal control over financial reporting which are      reasonably likely to adversely affect the registrant's ability to record,      process, summarize and report financial information;    and |
|----------------|---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

| ii.   | Any fraud, whether or not material, that involves management      or other employees who have a significant role in the registrant's      internal control over financialreporting. |
|-----------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|

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