Odorant receptors (ORs) and vomeronasal receptors (V1Rs and V2Rs) are large superfamilies of chemosensory receptors. As an extension of previous research using the 2001 Celera mouse genome assembly, we analyzed OR and V1R genes in the 2002 public mouse genome assembly. We identified 1403 OR genes (1068 potentially intact) and 332 V1R genes (164 potentially intact) in this C57BL/6J mouse genome. This expands the mouse OR and V1R superfamilies by adding approximately 100 OR and approximately 40 V1R potentially intact genes. The description of the genomic distribution of OR genes is more complete and accurate, and two major errors in OR gene distribution in the 2001 Celera assembly were corrected. For the first time, the complete genomic distribution of V1R genes was investigated in detail and placed in context with that of OR genes. V1R genes, like OR genes, tend to form clusters of similar genes in the genome. Comparison between the two genome assemblies revealed a high rate of single-nucleotide polymorphisms (SNPs) in both OR and V1R genes. The high ratio of nonsynonymous SNPs over synonymous SNPs in V1R genes suggests positive selection for these genes, possibly favoring species-specific and strain-specific pheromone detection. In addition, detailed analysis of the SNP rate aided in the identification of key residues in ORs.