Amplified Fragment Length Polymorphism (AFLP) fingerprinting was used to detect geneticudvariability in two stocks of common carps (Majalaya carp and Sinyonya carp) and secondudgeneration gynogens derived from the Majalaya carp. Primer combinations, E-AAC/M-CAA, EAGG/udM-CAC and E-ACC/M-CTT yielded 299 selectively amplified loci of which 66.2% wereudpolymorphic. Maximum polymorphism was evident in the Majalaya carp and minimum amongudthe gynogens. Four types of AFLP bands which were useful to differentiate the stocks in questionudwere identified. Band Sharing Index (BSI) matrix was generated from the band binaryudvalue sets. Maximum average BSI was exhibited by the gynogens and minimum by theudMajalaya carp. Inter-stock comparisons showed the gynogens to be closest to the Majalaya andudfarthest from the Sinyonya stock.
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