The Chinese striped-necked turtleMauremys sinensiswas first reported in the wild in South Korea in 2012. Owing to its potential to hybridize with the native and endangeredMauremys reevesiiin South Korea, leading to ecosystem disturbance,M. sinensiswas designated as an ecosystem-disturbing species (EDS; hereafter) in 2020. Such hybridization betweenM. sinensisandM. reevesiihas previously been reported in Taiwan. To protect and conserve the native South KoreanM. reevesiipopulation, the extent of its hybridization needed to be examined. Therefore, we developed novel high-resolution melting markers to elucidate the status of hybridization betweenMauremys sinensisandMauremys reevesiiin South Korea. We identified the presence ofM. sinensis,M. reevesii, and their hybrid across 47 sites in South Korea. Among these sites, five locations were confirmed as areas of sympatry for bothM. sinensisandM. reevesii, with one hybrid individual identified at the Jeonju-si site. In total, hybrids were identified at four different sites. For more definitive species identification, blood samples were collected from the specimens and subjected to mitochondrial DNA (mtDNA) cytochrome c oxidase subunit I (COI) gene and nuclear DNA (nDNA)R35gene analysis, leading to the identification of two more hybrids from two other sites. To date, no hybrids ofM. sinensishave been confirmed to reproduce in the wild, yet this requires further research for validation. The high-resolution melting (HRM) marker in theR35gene developed in this study yielded three distinct curves that were designated asM. sinensis,M. reevesii, andM. sinensis×M. reevesii, aligning with those of theR35gene sequencing. The novel markers developed in this study serve as a valuable tool that can be used in future research on rapid detection of hybridization.