The Chelonia face an extinction crisis, particularly in Asia: unsustainable harvests, and habitat fragmentation and loss accompanying rapid urbanization and land development all pose threats to turtles. These threats are particularly acute for those species with a high commercial value such as the yellow-margined box turtle Cuora flavomarginata. Because of burgeoning demand in the food and pet markets, combined with extensive habitat loss, C. flavomarginata is categorized as Endangered on the IUCN Red List. To investigate the status and distribution of this species in Taiwan we conducted an extensive trapping survey in 2001–2008, locating a total of 527 different individuals at 23 sites. Our results show that C. flavomarginata is restricted to low-elevation forested hills. Populations in lowland areas may have been extirpated by land development. There are four clusters of localities in low-elevation primary and secondary forests, and some relatively large populations survive. However, capture success at most sites was low. In those sites where we trapped > 20 individuals, sex ratios were significantly skewed towards females and adults predominated. The most essential measure for the conservation of C. flavomarginata in Taiwan is to secure and preserve some relatively undisturbed habitats at low elevations.