Overexploitation, habitat destruction, human-driven climate change and disease spread are resulting in the extinction of innumerable species, with amphibians being hit harder than most other groups [1]. Few species of amphibians are widespread, and those that are often represent complexes of multiple cryptic species. This is especially true for range-restricted salamanders [2]. Here, we used the widespread and critically endangered Chinese giant salamander (Andrias davidianus) to show how genetically uninformed management efforts can negatively affect species conservation. We find that this salamander consists of at least five species-level lineages. However, the extensive recent translocation of individuals between farms, where the vast majority of extant salamanders now live, has resulted in genetic homogenization. Mitochondrial DNA (mtDNA) haplotypes from northern China now predominate in farms. Unfortunately, hybrid offspring are being released back into the wild under well-intentioned, but misguided, conservation management. Our findings emphasize the necessity of genetic assessments for seemingly well-known, widespread species in conservation initiatives. Species serve as the primary unit for protection and management in conservation actions [3], so determining the taxonomic status of threatened species is a major concern, especially for amphibians. The level of threat to amphibians may be underestimated, and existing conservation strategies may be inadvertently harmful if conducted without genetic assessment.

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Over recent decades, Chinese giant salamanders Andrias spp. have declined dramatically across much of their range. Overexploitation and habitat degradation have been widely cited as the cause of these declines. To investigate the relative contribution of each of these factors in driving the declines, we carried out standardized ecological and questionnaire surveys at 98 sites across the range of giant salamanders in China. We did not find any statistically significant differences between water parameters (temperature, dissolved oxygen, ammonia, nitrite, nitrate, salinity, alkalinity, hardness and flow rate) recorded at sites where giant salamanders were detected by survey teams and/or had been recently seen by local respondents, and sites where they were not detected and/or from which they had recently been extirpated. Additionally, we found direct and indirect evidence that the extraction of giant salamanders from the wild is ongoing, including within protected areas. Our results support the hypothesis that the decline of giant salamanders across China has been primarily driven by overexploitation. Data on water parameters may be informative for the establishment of conservation breeding programmes, an initiative recommended for the conservation of these species.