The mammalian Sry on the short arm of the Y chromosome encodes a nuclear factor-like protein harboring a DNA-binding domain known as the HMG box. The Sox genes encode similar factor like proteins, but the sequence similarity of the HMG box to that of Sry is variable as being at least 60%. The functional relationship of Sox to Sry genes with special reference to sex determination is unclear except for a few items such as human autosomal Sox9. Thus, it is significant to know more about the evolutionary in addition to the functional relationship between Sry and Sox genes for deepening and broadening our understanding concerning primary sex determination. Therefore, to clarify the ancestry and molecular evolution of the mammalian sex determining gene Sry with its evolutionary relationships to the Sox gene, a molecular phylogenetic tree for the HMG box superfamily was constructed and analyzed, and the following conclusions were reached: (1) The nuclear non histone HMG proteins are supposedly the oldest, appearing at least more than one billion years ago, before the divergence of animals and plants. They diverged into two subgroups: one contains HMG14 and HMG17, and the other one contains HMG1 and HMG2 with various other genes. Subsequent divergences include the nucleolar UBF, nuclear SSRP as well as fungal mating protein Mc, MAT and Ste11. (2) The Sox and Sry genes diverged following the diversification of lymphoid transcription factors TCF and LEF. The Sry gene might have definitely evolved from the Sox gene cluster a few hundred million years ago. Additionally, the marsupial Sry, e.g. from Wallabie's and Dunnart's, is distinguished by being distant from eutherian Sry, but being closely related to the Sox gene cluster. (3) Molecular evolutionary rates estimated in mammalian Sry as the divergent rate per 100 million years are much higher than in Sox genes or other genes from the HMG box superfamily. This rapid evolution of Sry might agree with the fact that the Srys are present not on the pseudoautosomal region but on the distal region with no recombination of the Y chromosomal short arm.