Sec Form 4 Filing - HARTNETT JOSEPH M @ MERCURY COMPUTER SYSTEMS INC - 2006-09-11

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 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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1. Name and Address of Reporting Person HARTNETT JOSEPH M 2. Issuer Name and Ticker or Trading Symbol MERCURY COMPUTER SYSTEMS INC [ MRCY] 5. Relationship of Reporting Person(s) to Issuer (Check all applicable) _____ Director _____ 10% Owner X __ Officer (give title below) _____ Other (specify below) VP, Finance (Last) (First) (Middle) 3 WHITTEMORE TERRACE 3. Date of Earliest Transaction (MM/DD/YY) 09/11/2006 (Street) ANDOVER, MA01810 4. If Amendment, Date Original Filed (MM/DD/YY) 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 (MM/DD/YY) 2A. Deemed Execution Date, if any (MM/DD/YY) 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 09/11/2006 A 3,750 A $ 0 ( 1 ) 10,276 D

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 (MM/DD/YY) 3A. Deemed Execution Date, if any (MM/DD/YY) 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 (MM/DD/YY) 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 Employee Stock Option (right to buy) $ 23.46 09/11/2006 D 15,000 07/28/2005( 2 ) 07/28/2014 Common 15,000 $ 0 ( 3 ) 0 D

Reporting Owners Reporting Owner Name / Address Relationships Director 10% Owner Officer Other HARTNETT JOSEPH M 3 WHITTEMORE TERRACE ANDOVER, MA01810 VP, Finance Signatures Craig Barrows, Attorney-in-fact 09/12/2006 Signature of Reporting Person Date

Explanation of Responses:

( 1 )On September 11, 2006, Mercury Computer Systems, Inc., cancelled, pursuant to its option exchange program, an option granted to the reporting person on July 28, 2004. In exchange for the option , the reporting person received a restricted stock award covering 3,750 shares which vests as to two-thirds of the covered shares on September 11, 2008 and one-third of the covered shares on September 11, 2009. ( 2 )The cancelled option provide for vesting in four equal installments commencing on July 28, 2005. ( 3 )Field N/A to this transaction but was completed to allow for electronic filing only.

Reminder: Report on a separate line for each class of securities beneficially owned directly or indirectly.

* 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).

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