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The objective of this study was to investigate 4 aquaculture populations Shanghai (SH), Hangzhou (HZ), Kaihua (KH) and Xianju (XJ) and one wild population Yingshan (YS) of spotted barbell (Hemibarbus maculates) to assess their genetic diversity level and investigate the genetic structure of the populations. The dendrogram and STRUCTURE revealed that the populations XJ, KH, and HZ jointly formed one cluster, to which the populations SH and YS were sequentially adhered. The genetic diversity of the cultured populations maintained better, possible due to favourable hatchery conditions that decreased the effect of environmental selection present in wild populations. The results of the present study will contribute to the management of spotted barbell genetic resources, but also demonstrates how the genetic diversity of freshwater species is vulnerable to human activity.