The sex determination mechanism for the Chinese soft-shelled turtle (Pelodiscus sinensis) is subject to controversy. Some populations have been shown to possess sex chromosomes and thus genotypic sex determination (GSD), while others were reported to exhibit temperature-dependent sex determination (TSD). To test whether TSD and GSD coexist in this species or whether populations differ in their sex-determining system, we conducted egg incubation experiments to investigate how temperature influences hatchling sex in a wide range of populations of this species in China. In parallel, we used comparative genome hybridization (CGH) to study the micro-sex chromosomes of adult P. sinensis in the 2 populations that were previously identified to be TSD. The incubation experiments showed that temperature did not affect hatchling sex in any of the studied populations. CGH indicated that turtles have micro-sex chromosomes of the female heterogametic (ZZ/ZW) system in the 2 disputed populations. These results indicate that P. sinensis is a GSD rather than a TSD species. Thus, the apparent coexistence of TSD and GSD in this species is the result of previous misdiagnosis in purportedly TSD populations.