Field surveys in Taiwan have uncovered turtles presumed to be hybrids based on their intermediate morphology. We sequenced a mitochondrial (ND4) and nuclear (R35) gene of two putative hybrid individuals, along with representatives of the potential parental species (Mauremys mutica, M. reevesii, M. sinensis), to determine their genetic identity. Based on our data, both individuals are hybrids, with independent, recent origins resulting from the mating of a female M. reevesii and a male M. sinensis. Since we question whether the highly traded M. reevesii is endemic to Taiwan, this hybridization could represent human-mediated genetic pollution. We also discuss the implications of our findings on turtle conservation in Taiwan.