The DM domain gene families encode putative transcription factors related to the sexual regulators dsx from Drosophila melanogaster and mab-3 from Caertorhabditis elegans. DMRT genes were first identified as genes involved in sexual development in very distant metazoan phyla, but some of them were later shown to be involved in the somite or neuro system development in the embryo development. So different DMRT genes must play distinct roles,just the exact function mechanisms of the great majority of them,especially those of vertebrates DMRT genes,remain unclear. For example,we know really little about their upstream regulators and downstream targets.DM domain genes underwent frequent independent events of gene duplication during the course of evolution and the number of DMRT genes differs between phyla even within vertebrate lineage. Thanks to the existing genomic data of different species, we can compare the adjacent regions of DMRT genes (from DMRT1 to DMRT5) from different teleost fishes. In this study,we fully utilize the genomic data that we can get free from the website and use the well established method in comparing large genome sequences to analyze the relationship between different DMRT containing segments from different species genomes.Firstly, we compared the DMRT1-3-2 cluster containing chromosome segments from different fish species with those from tetrapods,and proved the fact that descended from one common chromosome segment before the divergence of rayfinned fish and tetrapods. When we further performed the linkage analysis of this region, we also identified three genes of SNF2, LDLR and ANKRD15 which were conserved in all the vertebrates we analyzed here. And the most interesting thing was that the SNF2 gene was closely linked to some DMRT genes across very distant metazoan phyla. The comparative sequence analysis also proved the orthologous relationships between DMRT4 or DMRT5 genes of different vertebrates, and the results uncovered an ancient chromosome duplication (or segmental duplication) event happened to the common ancestor of vertebrates DMRT4 and DMRT5 genes. Furthermore, we identified lots of genes including elavL genes that might have functions of close relationships with DMRT4 and DMRT5 by investigating their linked genes in different vertebrates, which further provided clues for in depth studies about the functions of DMRT family.