-----BEGIN PRIVACY-ENHANCED MESSAGE-----
Proc-Type: 2001,MIC-CLEAR
Originator-Name: webmaster@www.sec.gov
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<SEC-DOCUMENT>0001140361-09-024087.txt : 20091029
<SEC-HEADER>0001140361-09-024087.hdr.sgml : 20091029
<ACCEPTANCE-DATETIME>20091029171751
ACCESSION NUMBER:		0001140361-09-024087
CONFORMED SUBMISSION TYPE:	4
PUBLIC DOCUMENT COUNT:		1
CONFORMED PERIOD OF REPORT:	20091028
FILED AS OF DATE:		20091029
DATE AS OF CHANGE:		20091029

REPORTING-OWNER:	

	OWNER DATA:	
		COMPANY CONFORMED NAME:			Bissinger Ron
		CENTRAL INDEX KEY:			0001359029

	FILING VALUES:
		FORM TYPE:		4
		SEC ACT:		1934 Act
		SEC FILE NUMBER:	001-14257
		FILM NUMBER:		091145396

	MAIL ADDRESS:	
		STREET 1:		2401 MERCED STREET
		CITY:			SAN LEANDRO
		STATE:			CA
		ZIP:			94577

ISSUER:		

	COMPANY DATA:	
		COMPANY CONFORMED NAME:			ALPHA INNOTECH CORP
		CENTRAL INDEX KEY:			0000830736
		STANDARD INDUSTRIAL CLASSIFICATION:	LABORATORY ANALYTICAL INSTRUMENTS [3826]
		IRS NUMBER:				581729436
		STATE OF INCORPORATION:			DE
		FISCAL YEAR END:			1231

	BUSINESS ADDRESS:	
		STREET 1:		2401 MERCED ST.
		CITY:			SAN LEANDRO
		STATE:			CA
		ZIP:			94577
		BUSINESS PHONE:		5104839620

	MAIL ADDRESS:	
		STREET 1:		2401 MERCED ST.
		CITY:			SAN LEANDRO
		STATE:			CA
		ZIP:			94577

	FORMER COMPANY:	
		FORMER CONFORMED NAME:	XTRANA INC
		DATE OF NAME CHANGE:	20010702

	FORMER COMPANY:	
		FORMER CONFORMED NAME:	BIOPOOL INTERNATIONAL INC
		DATE OF NAME CHANGE:	19920703

	FORMER COMPANY:	
		FORMER CONFORMED NAME:	CYTRX BIOPOOL LTD
		DATE OF NAME CHANGE:	19890716
</SEC-HEADER>
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<TYPE>4
<SEQUENCE>1
<FILENAME>doc1.xml
<DESCRIPTION>FORM 4
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    <schemaVersion>X0303</schemaVersion>

    <documentType>4</documentType>

    <periodOfReport>2009-10-28</periodOfReport>

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    <issuer>
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        <issuerName>ALPHA INNOTECH CORP</issuerName>
        <issuerTradingSymbol>APNO.OB</issuerTradingSymbol>
    </issuer>

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            <rptOwnerName>Bissinger Ron</rptOwnerName>
        </reportingOwnerId>
        <reportingOwnerAddress>
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            <rptOwnerStreet2></rptOwnerStreet2>
            <rptOwnerCity>SAN LEANDRO</rptOwnerCity>
            <rptOwnerState>CA</rptOwnerState>
            <rptOwnerZipCode>94577</rptOwnerZipCode>
            <rptOwnerStateDescription></rptOwnerStateDescription>
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        <reportingOwnerRelationship>
            <isDirector>1</isDirector>
            <isOfficer>1</isOfficer>
            <isTenPercentOwner>0</isTenPercentOwner>
            <isOther>0</isOther>
            <officerTitle>CEO &amp; COO</officerTitle>
            <otherText></otherText>
        </reportingOwnerRelationship>
    </reportingOwner>

    <nonDerivativeTable>
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            <transactionDate>
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            </transactionDate>
            <deemedExecutionDate></deemedExecutionDate>
            <transactionCoding>
                <transactionFormType>4</transactionFormType>
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            <transactionTimeliness>
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            <transactionAmounts>
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                <transactionPricePerShare>
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            <expirationDate>
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                <transactionPricePerShare>
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            <transactionCoding>
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            <transactionAmounts>
                <transactionShares>
                    <value>100000</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0.52</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
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            <exerciseDate>
                <footnoteId id="F4"/>
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            <expirationDate>
                <value>2018-06-16</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
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                <underlyingSecurityShares>
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        <derivativeTransaction>
            <securityTitle>
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            <conversionOrExercisePrice>
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                <value>2009-10-28</value>
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                <value></value>
            </transactionTimeliness>
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                <transactionShares>
                    <value>100000</value>
                </transactionShares>
                <transactionPricePerShare>
                    <value>0.62</value>
                </transactionPricePerShare>
                <transactionAcquiredDisposedCode>
                    <value>D</value>
                </transactionAcquiredDisposedCode>
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            <exerciseDate>
                <footnoteId id="F5"/>
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            <expirationDate>
                <value>2019-09-01</value>
            </expirationDate>
            <underlyingSecurity>
                <underlyingSecurityTitle>
                    <value>Common Stock</value>
                </underlyingSecurityTitle>
                <underlyingSecurityShares>
                    <value>100000</value>
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                    <value>0</value>
                </sharesOwnedFollowingTransaction>
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            <ownershipNature>
                <directOrIndirectOwnership>
                    <value>D</value>
                </directOrIndirectOwnership>
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        </derivativeTransaction>
    </derivativeTable>

    <footnotes>
        <footnote id="F1">Disposed of pursuant to a merger agreement between the Issuer and Cell Biosciences, Inc. in exchange for a cash payment of $1.50 per share on the effective date of the merger.</footnote>
        <footnote id="F2">This option, which provided for vesting at the rate of 25% after one year and monthly vesting of the remainder in equal installments over the following three years, was canceled on the effective date of the merger.</footnote>
        <footnote id="F3">This option, which provided for vesting at the rate of 25% after one year and monthly vesting of the remainder in equal installments over the following three years, was canceled in the merger in exchange for a cash payment of $27,000, representing the difference between the exercise price of the option and the merger price ($1.50 per share).</footnote>
        <footnote id="F4">This option, which provided for monthly vesting in equal installments over four years, was canceled in the merger in exchange for a cash payment of $52,000, representing the difference between the exercise price of the option and the merger price ($1.50 per share).</footnote>
        <footnote id="F5">This option, which provided for vesting at the rate of 25% after one year and monthly vesting of the remainder in equal installments over the following three years, was canceled in the merger in exchange for a cash payment of $62,000, representing the difference between the exercise price of the option and the merger price ($1.50 per share).</footnote>
    </footnotes>

    <remarks></remarks>

    <ownerSignature>
        <signatureName>/s/ Ron Bissinger</signatureName>
        <signatureDate>2009-10-29</signatureDate>
    </ownerSignature>
</ownershipDocument>
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</TEXT>
</DOCUMENT>
</SEC-DOCUMENT>
-----END PRIVACY-ENHANCED MESSAGE-----