We investigated a sample of apparently unique frogs from Sado Island, Japan. While being tentatively identified to Rana rugosa on the basis of general morphological resemblance, this form (yellow type) differs from the typical Japanese R. rugosa by showing deep yellow or orange coloration in abdomen and the ventral surfaces of legs, and by having much smoother skin on the entire body. For the Japanese populations of Rana rugosa, following four genetic forms are currently recognized: Kanto form (around Tokyo and northeastern Japan), Western Japan form (western Japan), XY form (central Japan), and ZW form (northwestern Japan). Of these, the latter two forms bear differentiated sex chromosomes of XX/XY and ZZ/ZW types, respectively, and are assumed to have originated through hybridizations between the former two forms. In order to infer the phylogenetic affinity of the yellow type from Sado Island, we examined the karyotype and also analyzed the mitochondrial gene sequences. Our results strongly suggested that the yellow type had originated from the ancestral lineage of the Kanto form early in the divergence of R. rugosa in Japan, achieving genetic characteristics of its own. Also, the results suggested distant affinity of the ZW form to the yellow type, despite their geographic proximity.