A method of comparative gene mapping, in which PCR fragments from a species in which the gene sequence is known, forms an interspecies hybrid, a xenoduplex, with a PCR fragment from a species in which the gene has not been identified. The presence of the xenoduplex is detected by its size, therefore its electrophoretic mobility, being somewhat different from that of either of the homoduplices. The method relies on the sequences of the two species being sufficiently similar so that primers designed for the sequence of one species’ gene will hybridize to the template of the other species, and that the xenoduplex will be sufficiently stable to be formed and survive electrophoretic separation. When a panel of narrowly selected fragments of chromosomes from one species reacts positively by this test with a recognized gene fragment from another species, the assignment of the gene can be made to the chromosome region from which the panel was taken.