Amphibians employ genetic sex determination systems with male and female heterogamety. The ancestral state of sex determination in amphibians has been suggested to be female heterogamety; however, the origins of the sex chromosomes and the sex-determining genes are still unknown. In Xenopus laevis, chromosome 3 with a candidate for the sex- (ovary-) determining gene (DM-W) was recently identified as the W sex chromosome. This study conducted comparative genomic hybridization for X. laevis and Xenopus tropicalis and FISH mapping of eight sexual differentiation genes for X. laevis, X. tropicalis, and Rana rugosa. Three sex-linked genes of R. rugosa--AR, SF-1/Ad4BP, and Sox3--are all localized to chromosome 10 of X. tropicalis, whereas AR and SF-1/Ad4BP are mapped to chromosome 14 and Sox3 to chromosome 11 in X. laevis. These results suggest that the W sex chromosome was independently acquired in the lineage of X. laevis, and the origins of the ZW sex chromosomes are different between X. laevis and R. rugosa. Cyp17, Cyp19, Dmrt1, Sox9, and WT1 were localized to autosomes in X. laevis and R. rugosa, suggesting that these five genes probably are not candidates for the sex-determining genes in the two anuran species.