We have determined the chromosomal locations of the human and murine genes coding for alpha 2(IX) collagen, a polypeptide subunit of the heterotrimeric type IX collagen molecule. COL9A2 was mapped to human chromosome 1p32.3-p33 using fluorescence in situ hybridization. A single-strand conformational polymorphism within the murine Col9a2 gene was used to map this locus to mouse chromosome 4. We also present new sequence data, which completes the coding information for the human alpha 2(IX) chain and revises the sequence for the chicken alpha 2(IX) chain. This permits comparison of the carboxyl-terminal (NC1) domains of the alpha 1(IX), alpha 2(IX), and alpha 3(IX) chains across several species.