The SRY (sex determining region on the Y chromosome) gene has an important role in sex determination and shows a strict paternal mode of inheritance. To better understand evolutionary changes in the gene structure and their phylogenetic utility, complete sequences of the SRY region (591-651 bp) spanning from the initiation codon (ATG) to the stop codon of TAG were determined in 20 cetacean species, covering two families of suborder Mysticeti and six families of suborder Odonticeti. The HMG (high mobility group) box (231 bp), a DNA binding motif, was highly conserved in the cetacean SRY sequences. In contrast, seven synonymous substitutions and 12 nonsynonymous substitutions were detected in the N-terminal region (156 bp). The C-terminal region was heterogeneous in length (216-261 bp). One base insertion at the end of the HMG box, which resulted in a frame-shift in the C-terminal region, was detected in superfamily Delphinoidea. Further sequence determination (171-175 bp) in the 5' flanking region of the SRY gene revealed the presence of an element of "GGGGGCGG", the consensus motif of Sp1 (specificity protein 1), in the predicted promoter region. Paternal lineage relationships inferred from these SRY sequences were concordant with previous phylogenetic inferences in the literature, using other gene markers.