Ownership Submission
FORM 4
Check this box if no longer subject to Section 16. Form 4 or Form 5 obligations may continue. See Instruction 1(b).
UNITED STATES SECURITIES AND EXCHANGE COMMISSION
Washington, D.C. 20549

STATEMENT OF CHANGES IN BENEFICIAL OWNERSHIP OF SECURITIES

Filed pursuant to Section 16(a) of the Securities Exchange Act of 1934, Section 17(a) of the Public Utility Holding Company Act of 1935 or Section 30(h) of the Investment Company Act of 1940
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(Print or Type Responses)
1. Name and Address of Reporting Person *
MARAGANORE JOHN
   2. Issuer Name and Ticker or Trading Symbol
ALNYLAM PHARMACEUTICALS, INC. [ALNY] 		5. Relationship of Reporting Person(s) to Issuer
(Check all applicable)
__X__ Director _____ 10% Owner
__X__ Officer (give title below) _____ Other (specify below)
CEO
(Last)
(First)
(Middle)
300 THIRD ST		 3. Date of Earliest Transaction (Month/Day/Year)
06/16/2009
(Street)

CAMBRIDGE, MA 02139		 4. If Amendment, Date Original Filed(Month/Day/Year)
 6. Individual or Joint/Group Filing(Check Applicable Line)
_X_ Form filed by One Reporting Person
___ Form filed by More than One Reporting Person
(City)
(State)
(Zip)
Table I - Non-Derivative Securities Acquired, Disposed of, or Beneficially Owned
1.Title of Security
(Instr. 3)		 2. Transaction Date (Month/Day/Year) 2A. Deemed Execution Date, if any (Month/Day/Year) 3. Transaction Code
(Instr. 8)		 4. Securities Acquired (A) or Disposed of (D)
(Instr. 3, 4 and 5)		 5. Amount of Securities Beneficially Owned Following Reported Transaction(s)
(Instr. 3 and 4)		 6. Ownership Form: Direct (D) or Indirect (I)
(Instr. 4)		 7. Nature of Indirect Beneficial Ownership
(Instr. 4)
Code V Amount (A) or (D) Price
Common Stock 06/16/2009   M(1)   39,600 A $ 0.475 39,600 D  
Common Stock 06/16/2009   S(2)   39,600 D $ 21.4325 (3) 0 D  
Common Stock 06/16/2009   M(1)   400 A $ 0.475 400 D  
Common Stock 06/16/2009   S(2)   400 D $ 22.1575 (4) 0 D  
Common Stock 06/17/2009   M(1)   40,000 A $ 0.475 40,000 D  
Common Stock 06/17/2009   S(2)   40,000 D $ 21.396 (5) 0 D  
Common Stock 06/18/2009   M(1)   11,800 A $ 0.475 11,800 D  
Common Stock 06/18/2009   S(2)   11,800 D $ 21.3662 (6) 0 D  
Common Stock 06/18/2009   M(1)   28,200 A $ 0.475 28,200 D  
Common Stock 06/18/2009   S(2)   28,200 D $ 21.3662 (6) 0 D  
Common Stock               1,020 I by Managed Account (7)

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Table II - Derivative Securities Acquired, Disposed of, or Beneficially Owned
(e.g., puts, calls, warrants, options, convertible securities)
1. Title of Derivative Security
(Instr. 3)		 2. Conversion or Exercise Price of Derivative Security 3. Transaction Date (Month/Day/Year) 3A. Deemed Execution Date, if any (Month/Day/Year) 4. Transaction Code
(Instr. 8)		 5. Number of Derivative Securities Acquired (A) or Disposed of (D)
(Instr. 3, 4, and 5)		 6. Date Exercisable and Expiration Date
(Month/Day/Year)		 7. Title and Amount of Underlying Securities
(Instr. 3 and 4)		 8. Price of Derivative Security
(Instr. 5)		 9. Number of Derivative Securities Beneficially Owned Following Reported Transaction(s)
(Instr. 4)		 10. Ownership Form of Derivative Security: Direct (D) or Indirect (I)
(Instr. 4)		 11. Nature of Indirect Beneficial Ownership
(Instr. 4)
Code V (A) (D) Date Exercisable Expiration Date Title Amount or Number of Shares
Non Qualified Stock Option $ 0.475 06/16/2009   M(1)     39,600 12/09/2003 02/26/2013 Common Stock 39,600 $ 0 52,200 D  
Non Qualified Stock Option $ 0.475 06/16/2009   M(1)     400 12/09/2003 02/26/2013 Common Stock 400 $ 0 51,800 D  
Non Qualified Stock Option $ 0.475 06/17/2009   M(1)     40,000 12/09/2003 02/26/2013 Common Stock 40,000 $ 0 11,800 D  
Non Qualified Stock Option $ 0.475 06/18/2009   M(1)     11,800 12/09/2003 02/26/2013 Common Stock 11,800 $ 0 0 D  
Incentive Stock Option $ 0.475 06/18/2009   M(1)     28,200 12/09/2003 02/26/2013 Common Stock 28,200 $ 0 64,102 D  

Reporting Owners

Reporting Owner Name / Address Relationships
 Director  10% Owner  Officer  Other
MARAGANORE JOHN
300 THIRD ST
CAMBRIDGE, MA 02139		   X     CEO  

Signatures

 /s/ Patricia L Allen, Attorney-in-Fact for John M Maraganore   06/18/2009
**Signature of Reporting Person Date

Explanation of Responses:

* If the form is filed by more than one reporting person, see Instruction 4(b)(v).
** Intentional misstatements or omissions of facts constitute Federal Criminal Violations. See 18 U.S.C. 1001 and 15 U.S.C. 78ff(a).
(1) The exercises reported on this Form 4 were made pursuant to a Rule 10b5-1 trading plan adopted by the reporting person on March 10, 2009.
(2) The sales reported on this Form 4 were made pursuant to a Rule 10b5-1 trading plan adopted by the reporting person on March 10, 2009.
(3) Sales prices ranged from $21.06 to $22.05.
(4) Sales prices ranged from $22.09 to $22.27.
(5) Sales prices ranged from $21.12 to 21.52.
(6) Sales prices ranged from $21.11 to $21.68.
(7) The reporting person owns 1,020 shares of ALNY common stock under the ALNY 401(k) Plan as a result of the ALNY 401(k) matching contribution program.

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