Inter-simple sequence repeat (ISSR) markers were used to determine the genetic variation and genetic differentiation of cultured and wild populations of Trachidermus fasciatus, an endangered catadromous fish species in China. Six selected primers were used to amplify DNA samples from 85 individuals, and 353 loci were detected. Relatively low genetic diversity was detected in the cultured population (the percentage of polymorphic loci PPL = 73.80%, Nei’s gene diversity h = 0.178 2, Shannon information index I = 0.276 9). However, the genetic diversity at the species level was relatively high (PPL = 91.78%; h = 0.258 3, I = 0.398 6). The UPGMA tree grouped together the genotypes almost according to their cultured and wild origin, showing distinct differences in genetic structure between wild and cultured populations. The pairwise Fst values confirmed significant genetic differentiation between wild and cultured samples. The cultivated population seems to be low in genetic diversity as a result of detrimental genetic effects in the captive population. The results suggest that ISSR markers are effective for rapid assessment of the degree of diversity of a population, thus giving important topical information relevant to preserving endangered species. Inter-simple sequence repeat (ISSR) markers were used to determine the genetic variation and genetic differentiation of cultured and wild populations of Trachidermus fasciatus, an endangered catadromous fish species in China. Six selected primers were used to amplify DNA samples from 85 individuals, and 353 loci were detected. Relatively low genetic diversity was detected in the cultured population (the percentage of polymorphic loci PPL = 73.80%, Nei’s gene diversity h = 0.178 2, Shannon information index I = 0.276 9). However, the genetic diversity at the The UPGMA tree grouped together the genotypes almost according to their cultured and wild origin, showing distinct differences in genetic structure between wild and cultured populations. The pairwise Fst values ​​confirmed significant genetic differentiation between wild and cultured samples. The cultivatedpopulation seems to be low in genetic diversity as a result of detrimental genetic effects in the captive population. The results suggest that ISSR markers are effective for rapid assessment of the degree of diversity of a population, thus giving important topical information relevant to preserving endangered species.