Freshwater turtles are one of the most threatened animal groups in the world, especially in Asia. The Beale’s Eyed Turtle ( Sacalia bealei ) is a highly endangered Chinese species at risk of extinction due to overexploitation for the food and pet trades. Nonetheless, Hong Kong still houses a handful of relatively healthy populations of this species, providing an increasingly rare opportunity to study the population genetics of wild populations and, in turn, guide conservation action. In this study, we used genome-wide double-digest restriction-site associated DNA sequencing (ddRADseq) markers to examine the population structure of S. bealei from all known wild individuals with samples suitable for DNA sequencing, representing a subset of its distribution in Hong Kong (two localities: HK1, HK2) and Fujian Province. Although genetic diversity is relatively low, we recovered four genetic clusters, with three corresponding to each of the three known localities (HK1, HK2, Fujian), and admixture between the clusters. Captive-breeding colony individuals showed mixed geographic origins, with approximately half clustering with Fujian populations and half with Hong Kong populations. These data were used to evaluate the genetic diversity and infer the geographic origin of an ex situ breeding colony with individuals of unknown provenance. These results provide important baseline information on the population structure of wild S. bealei and the potential geographic origins of captive turtles, which directly contribute to in situ and ex situ conservation efforts of the species.