The three peripheral subspecies of the house mouse Mus musculus have fixed specific variants of the androgen-binding protein (ABP) that have been proposed to be part of a recognition mechanism that could participate in sexual isolation between the subspecies. We tested for selection on Abpa by characterizing the pattern of Abpa introgression across a transect of the hybrid zone between M. m. musculus and M. m. domesticus in Jutland. On the musculus side, the cline for Abpa resembled that of a nearly neutral allozyme more than that of strongly selected X and Y chromosome markers. However, the high central step which displaces the tail of introgression of Abpa to higher frequencies was best accounted for by linkage to a locus under strong selection against hybrids. Still, we cannot exclude that this pattern results from weak selection against Abpa in the tail of introgression, which would be compatible with an assortative choice mechanism. On the domesticus side there was little introgression close to the hybrid zone, presumably due to a geographical barrier to migration. However, substantial frequencies of musculus alleles occurred further away, suggesting mixed colonization patterns as well as flow across the hybrid zone. © 2005 The Linnean Society of London, Biological Journal of the Linnean Society, 2005, 84, 447–459.