Mouse annexin III cDNA was characterized from I.M.A.G.E. Consortium (LLNL) expressed sequence tag clones by molecular sequencing, chromosomal mapping and systematic analysis. cDNA sequences extended the known 5' and 3' untranslated regions and confirmed the location of intron 7 with respect to the human gene. The Anx3 locus mapped to the middle of mouse chromosome 5 between Areg and Fgf5. Protein-coding regions were compared with homologous annexins to establish subfamily identity, structural conservation and divergence pattern. Annexin III exhibited low functional constraint against structural change and weak phylogenetic association with known annexins. The rapid, constant divergence of human and rodent annexins III from each other and from other annexin subfamilies was used to estimate gene separation times. Phylogenetic, phenetic and structural data suggested a possible direct or indirect separation of annexin III from XI approximately 317 million years ago.