-----BEGIN PRIVACY-ENHANCED MESSAGE-----
Proc-Type: 2001,MIC-CLEAR
Originator-Name: webmaster@www.sec.gov
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MIC-Info: RSA-MD5,RSA,
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 A4urYzQYubjRAjBesDKHpQ==

<SEC-DOCUMENT>0001181431-06-042426.txt : 20060718
<SEC-HEADER>0001181431-06-042426.hdr.sgml : 20060718
<ACCEPTANCE-DATETIME>20060718111609
ACCESSION NUMBER:		0001181431-06-042426
CONFORMED SUBMISSION TYPE:	4/A
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20060713
FILED AS OF DATE:		20060718
DATE AS OF CHANGE:		20060718

ISSUER:		

	COMPANY DATA:	
		COMPANY CONFORMED NAME:			MERCURY COMPUTER SYSTEMS INC
		CENTRAL INDEX KEY:			0001049521
		STANDARD INDUSTRIAL CLASSIFICATION:	ELECTRONIC COMPONENTS & ACCESSORIES [3670]
		IRS NUMBER:				042741391
		STATE OF INCORPORATION:			MA
		FISCAL YEAR END:			0630

	BUSINESS ADDRESS:	
		STREET 1:		199 RIVERNECK RD
		CITY:			CHELMSFORD
		STATE:			MA
		ZIP:			01824
		BUSINESS PHONE:		9782561300

	MAIL ADDRESS:	
		STREET 1:		199 RIVERNECK ROAD
		CITY:			CHELMSFORD
		STATE:			MA
		ZIP:			01824

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			SKALABRIN MARK F
		CENTRAL INDEX KEY:			0001211772

	FILING VALUES:
		FORM TYPE:		4/A
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	000-23599
		FILM NUMBER:		06966480

	MAIL ADDRESS:	
		STREET 1:		199 RIVERNECK ROAD
		CITY:			CHEISFORD
		STATE:			MA
		ZIP:			01824
</SEC-HEADER>
<DOCUMENT>
<TYPE>4/A
<SEQUENCE>1
<FILENAME>rrd124629.xml
<TEXT>
<XML>
<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0202</schemaVersion>

    <documentType>4/A</documentType>

    <periodOfReport>2006-07-13</periodOfReport>

    <dateOfOriginalSubmission>2006-07-14</dateOfOriginalSubmission>

    <notSubjectToSection16>0</notSubjectToSection16>

    <issuer>
        <issuerCik>0001049521</issuerCik>
        <issuerName>MERCURY COMPUTER SYSTEMS INC</issuerName>
        <issuerTradingSymbol>MRCY</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001211772</rptOwnerCik>
            <rptOwnerName>SKALABRIN MARK F</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>175 CRANE NECK ROAD</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>WEST NEWBURY</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>01985</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>VP, OEM Solutions Group</officerTitle>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2006-07-13</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>M</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>480</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>2.00</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>53510</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common Stock</value>
            </securityTitle>
            <transactionDate>
                <value>2006-07-13</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>M</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>11200</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>2.00</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>A</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>64710</value>
                    <footnoteId id="F1"/>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <derivativeTable>
        <derivativeTransaction>
            <securityTitle>
                <value>Incentive Stock Option (Right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>2.00</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2006-07-13</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>M</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>480</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0.00</value>
                    <footnoteId id="F2"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <value>2000-07-30</value>
            </exerciseDate>
            <expirationDate>
                <value>2006-07-30</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>480</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>0</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeTransaction>
        <derivativeTransaction>
            <securityTitle>
                <value>Incentive Stock Option (Right to buy)</value>
            </securityTitle>
            <conversionOrExercisePrice>
                <value>2.00</value>
            </conversionOrExercisePrice>
            <transactionDate>
                <value>2006-07-13</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>M</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>11200</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0.00</value>
                    <footnoteId id="F2"/>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <exerciseDate>
                <value>2001-09-09</value>
            </exerciseDate>
            <expirationDate>
                <value>2006-09-09</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>11200</value>
                </underlyingSecurityShares>
            </underlyingSecurity>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>0</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
            </ownershipNature>
        </derivativeTransaction>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">Includes 436 shares and 807 shares purchased through the Mercury Computer Systems, Inc. employee stock purchase plan in December 2005 and June 2006 respectively.</footnote>
        <footnote id="F2">Field N/A to this transaction but was completed to allow for electronic filing only.</footnote>
    </footnotes>

    <ownerSignature>
        <signatureName>Craig Barrows, Attorney-in-fact</signatureName>
        <signatureDate>2006-07-17</signatureDate>
    </ownerSignature>
</ownershipDocument>
</XML>
</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
-----END PRIVACY-ENHANCED MESSAGE-----