Sea turtles are globally endangered and face anthropogenic threats, such as direct harvest, bycatch, and habitat degradation. Genetic studies help identify connectivity between nesting and foraging grounds for conservation and management. However, information on genetic stock composition of green turtles (Chelonia mydas) in the South China Region (including Hong Kong, Guangdong Province, and Taiwan) is severely limited. In this study, mixed stock analysis based on the 760-bp mitochondrial DNA (mtDNA) control region of green turtles (n = 110) revealed that the primary source rookeries in the Pacific contributing to foraging green turtle aggregations in the South China Region were Peninsular Malaysia, Yap in the Federated States of Micronesia, Aru of Indonesia, Sulu Sea, northeastern Borneo, Republic of Marshall Islands, Wan-an of Taiwan, and the central Ryukyu and Yaeyama of Japan. This study is the first to investigate and report the source nesting populations of a relatively large number of foraging green turtles in the region. The genetic results also indicate possible use of coastal Guangdong, the Taiwan Strait, and the East China Sea as habitat by pelagic-phase green turtles hatched from nesting beaches in Taiwan and mainland China. As a precautionary approach for effective sea turtle conservation, conservation and management of each distinct green turtle source rookery as well as foraging aggregations sourced from multiple natal origins in the South China Region is needed to preserve genetic diversity for the species. Anthropogenic threats to nesting and foraging habitats and migratory pathways, such as direct take for trade and fishery impacts, should be thoroughly assessed and effectively mitigated by regional collaboration to sustain these populations.