-----BEGIN PRIVACY-ENHANCED MESSAGE-----
Proc-Type: 2001,MIC-CLEAR
Originator-Name: webmaster@www.sec.gov
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<SEC-DOCUMENT>0001012975-06-000019.txt : 20060120
<SEC-HEADER>0001012975-06-000019.hdr.sgml : 20060120
<ACCEPTANCE-DATETIME>20060120184805
ACCESSION NUMBER:		0001012975-06-000019
CONFORMED SUBMISSION TYPE:	4
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20060118
FILED AS OF DATE:		20060120
DATE AS OF CHANGE:		20060120

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			OXFORD BIOSCIENCE PARTNERS IV LP
		CENTRAL INDEX KEY:			0001140484
		STATE OF INCORPORATION:			DE
		FISCAL YEAR END:			1231

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	000-22570
		FILM NUMBER:		06541818

	BUSINESS ADDRESS:	
		STREET 1:		222 BERKELEY STREET
		STREET 2:		SUITE 1650
		CITY:			BOSTON
		STATE:			MA
		ZIP:			02116
		BUSINESS PHONE:		6173577474

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			MRNA FUND  II LP
		CENTRAL INDEX KEY:			0001161302

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	000-22570
		FILM NUMBER:		06541817

	BUSINESS ADDRESS:	
		STREET 1:		31 ST JAMES AVENUE
		STREET 2:		SUITE 905
		CITY:			BOSTON
		STATE:			MA
		ZIP:			02116
		BUSINESS PHONE:		617-357-7474

ISSUER:		

	COMPANY DATA:	
		COMPANY CONFORMED NAME:			Solexa, Inc.
		CENTRAL INDEX KEY:			0000913275
		STANDARD INDUSTRIAL CLASSIFICATION:	MEDICINAL CHEMICALS & BOTANICAL PRODUCTS [2833]
		IRS NUMBER:				943161073
		STATE OF INCORPORATION:			DE
		FISCAL YEAR END:			1231

	BUSINESS ADDRESS:	
		STREET 1:		25861 INDUSTRIAL BLVD
		CITY:			HAYWARD
		STATE:			CA
		ZIP:			94545
		BUSINESS PHONE:		5106709300

	MAIL ADDRESS:	
		STREET 1:		25861 INDUSTRIAL BLVD
		CITY:			HAYWARD
		STATE:			CA
		ZIP:			94545

	FORMER COMPANY:	
		FORMER CONFORMED NAME:	LYNX THERAPEUTICS INC
		DATE OF NAME CHANGE:	19931008
</SEC-HEADER>
<DOCUMENT>
<TYPE>4
<SEQUENCE>1
<FILENAME>edgar.xml
<DESCRIPTION>PRIMARY DOCUMENT
<TEXT>
<XML>
<?xml version="1.0"?>
<ownershipDocument>

    <schemaVersion>X0202</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2006-01-18</periodOfReport>

    <notSubjectToSection16>1</notSubjectToSection16>

    <issuer>
        <issuerCik>0000913275</issuerCik>
        <issuerName>Solexa, Inc.</issuerName>
        <issuerTradingSymbol>SLXA</issuerTradingSymbol>
    </issuer>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001140484</rptOwnerCik>
            <rptOwnerName>OXFORD BIOSCIENCE PARTNERS IV LP</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>222 BERKELEY ST.</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>BOSTON</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02116</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>1</isOther>
            <otherText>Former 10% Owner</otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <reportingOwner>
        <reportingOwnerId>
            <rptOwnerCik>0001161302</rptOwnerCik>
            <rptOwnerName>MRNA FUND  II LP</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
            <rptOwnerStreet1>222 BERKELEY ST.</rptOwnerStreet1>
            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>BOSTON</rptOwnerCity>
            <rptOwnerState>MA</rptOwnerState>
            <rptOwnerZipCode>02116</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
        </reportingOwnerAddress>
        <reportingOwnerRelationship>
            <isDirector>0</isDirector>
            <isOfficer>0</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>1</isOther>
            <otherText>Former 10% Owner</otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common</value>
            </securityTitle>
            <transactionDate>
                <value>2006-01-18</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>J</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
                <footnoteId id="F1"/>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>1980133</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>1035355</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value></value>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
        <nonDerivativeTransaction>
            <securityTitle>
                <value>Common</value>
            </securityTitle>
            <transactionDate>
                <value>2006-01-18</value>
            </transactionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
                <transactionCode>J</transactionCode>
                <equitySwapInvolved>0</equitySwapInvolved>
                <footnoteId id="F2"/>
            </transactionCoding>
            <transactionAmounts>
                <transactionShares>
                    <value>19867</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
            </transactionAmounts>
            <postTransactionAmounts>
                <sharesOwnedFollowingTransaction>
                    <value>10388</value>
                </sharesOwnedFollowingTransaction>
            </postTransactionAmounts>
            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>I</value>
                </directOrIndirectOwnership>
                <natureOfOwnership>
                    <value>By mRNA Fund II L.P.</value>
                </natureOfOwnership>
            </ownershipNature>
        </nonDerivativeTransaction>
    </nonDerivativeTable>

    <footnotes>
        <footnote id="F1">On January 18, 2006 Oxford Bioscience Partners IV L.P. (&quot;Oxford IV&quot;) distributed an aggregate of 1,980,133 shares of the Issuer's Common Stock to its partners for no consideration.  As a result of the distribution, Oxford IV no longer beneficially owns such distributed shares.</footnote>
        <footnote id="F2">On January 18, 2006 mRNA Fund II L.P. (&quot;mRNA&quot;) distributed an aggregate of 19,867 shares of the Issuer's Common Stock to its partners for no consideration.  As a result of the distribution, mRNA no longer beneficially owns such distributed shares.</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>/s/ Jonathan J. Fleming, as general partner of the general partner of Oxford Bioscience Partners IV L.P.</signatureName>
        <signatureDate>2006-01-20</signatureDate>
    </ownerSignature>

    <ownerSignature>
        <signatureName>/s/ Jonathan J. Fleming, as general partner of the general partner of mRNA Fund II L.P.</signatureName>
        <signatureDate>2006-01-20</signatureDate>
    </ownerSignature>
</ownershipDocument>
</XML>
</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
-----END PRIVACY-ENHANCED MESSAGE-----