Mouse salivary androgen-binding protein (ABP) is a major secretory product of the submaxillary glands. Although it is a common salivary protein among rodents generally, the function of ABP has yet to be determined. Here we report a comparison of the DNA coding sequences and putative amino acid sequences they determine for the three common alleles of the Alpha subunit gene (Abpa), alleles that appear to be diagnostic for the three subspecies of Mus musculus. Three other unique sequences were found in the species M. caroli, M. spretus, and M. spicilegus. Comparison of the six sequences shows that 8 of the 20 base substitution sites produce a high degree of variability in amino acids 32, 33, 36, and 39, a variability that creates unique sequence combinations in each species and subspecies. We compare the possibilities that selection or genetic drift caused this unusual microevolution and argue that selection is the more likely explanation. We speculate on the potential significance of this with respect to the proposal that ABP is involved in assortive mate kin selection.