We attempted to estimate the origin of the exotic frog Polypedates leucomystax in the Ryukyu Archipelago. This species was first found in 1964 just in front of the U.S. military base at Kadena on Okinawajima Island and currently has established feral populations on more than 20 islands. We conducted phylogenetic analyses using mitochondrial DNA sequences of the cytochrome b gene. Samples of P. leucomystax from five islands of the Ryukyus had a single haplotype, which was identical to that of a Philippine sample but quite different from haplotypes of Vietnamese samples. Samples of P. megacephalus from Taiwan formed a clade different from the P. leucomystax clade. From these results, P. leucomystax in the Ryukyus seems to have originated through accidental transportation of very few individuals with military cargo from somewhere around the Philippines.