Vertebrates contain a family of genes related to the Drosophila doublesex and C. elegans mab-3 genes, which encode transcription factors including a DNA-binding motif, DM domain. Evolution and function of different DMRT genes of vertebrates have not been understood yet,although some DM proteins are involved in sex determination, sexual differentiation and early embryonic development among different phyla. By genomic analysis of zebrafish and rat DMRT genes, all protein sequences of the vertebrate DMRTs were searched from gene databases and aligned. Phylogenetic tree of all these DMRT genes was reconstructed and evaluated by Bootstrap method. These DMRT genes were clustered into seven subfamilies. Results from analysis of gene structure and cluster organization of DMRT genes showed that synteny of DMRT genes of vertebrates were highly conserved among human, mouse, rat, fugu, medaka and zebrafish, with two syntenic groups, DMRT 1 approximately 3 and DMRT 5 approximately 6.