Sex determination in mammals is controlled by the Y-linked SRY gene, which encodes a transcription factor with a DNA-binding motif of the HMG type. The only conserved region in this gene is the HMG-box, whose nucleotide sequence is currently available in a number of mammalian taxa. However, nothing is known about this gene in bats. Here, we report partial sequences of the SRY HMG-box from four microbat and four megabat species. We used the SRY HMG- box sequences from micro- and megabats to test the phylogenetic relationships between microbats, megabats, and primates. In maximum parsimony and maximum-likelihood trees, mega- and microbat branches start in the same internal node, which is consistent with a monophyletic origin of this mammalian group.