Tanichthys albonubes is a cyprinid fish of South China and North Vietnam. Although this species has been sold worldwide in the aquarium trade for more than a century, it is listed as a second‐class state‐protected animal in China and classified as ‘extinct in nature’ in the China Red Data Book. To investigate the population history of T. albonubes and evaluate the genetic conditions among the wild and hatchery populations, mitochondrial genes (mtDNA, 2032 bp from the d‐loop and cyt b), nuclear genes (nuDNA, 2241 bp from RAG1 and ENC1) and 13 microsatellite loci were used to assess the genetic structure throughout the range of this species. In total, 358 specimens were collected from three hatcheries and all known wild populations. This study found that the discordant population structure among these genetic markers was accounted for by differences in the effective population sizes. The results indicated that (1) the three hatchery stocks originated from a single source in China and that the hatchery stock in China maintained almost all the T. albonubes genetic diversity in the downstream reaches of the Pearl River; (2) the wild population near Baiyun Mountain originated from hatchery releases; (3) the population history reflects the complex geological history of South China; and (4) the habitat destruction and fragmentation that have resulted in small and isolated populations may have shaped the genetic structure of T. albonubes. The low‐level genetic diversity of T. albonubes supports the need for conservation interventions. The geographically distinct genotypes indicate a need for the development of management strategies directed towards the conservation of localized populations. The genetic status of all populations, including the hatchery stocks, should be evaluated and monitored continuously.

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