The Reeves’ turtle, Mauremys reevesii, resides in freshwater bodies of Korea, China, Japan, and Taiwan, and is designated as an endangered species in the Republic of Korea (ROK). However, international pet trade among East Asian countries has made it difficult to identify the indigenous population of M. reevesii in the ROK. In this study, a genotyping marker targeting the mitochondrial cytochrome b (COB) region that easily distinguishes the Korean population was developed for high-resolution melting (HRM) analysis and applied to 27 blood samples obtained from diverse Korean freshwater bodies and pet trade markets. The HRM analysis produced three distinct HRM curves that were designated as the Korean Type, Chinese Type, and Minor Type, whose results exactly matched those of COB sequencing. Our genotyping method will be useful for the rapid and accurate identification of the native population of M. reevesii in the ROK.