The Japanese Pond Turtle, Mauremys japonica, and the Reeves' Pond Turtle, Mauremys reevesii, are common aquatic geoemydid species in Japan. The former is endemic to Japan, whereas the latter is distributed widely throughout East Asia, China, Korea, Taiwan, and Japan. Although the Japanese populations of M. reevesii were generally considered to be indigenous, it was suggested recently that Japanese M. reevesii is derived from multiple artificial introductions from elsewhere in Asia. Putative hybrid individuals, with intermediate morphological characters, have been observed in the wild. Furthermore, captive congeneric individuals have produced viable offspring that attained sexual maturity. To clarify the extent of hybridization between these species, we examined nuclear DNA and mitochondrial DNA genetic markers of putative hybrids collected in the field. We found that most of the animals assayed had nuclear DNA derived from both species. In addition, several individuals originated from hybrid mothers implying that hybridization is indeed occurring in the wild and that female hybrids are fertile and reproduce. Our results indicate an ongoing process of introgression of introduced M. reevesii alleles into the gene pool of native populations of M. japonica.