| Summary: | Recently, the economic traits of Chinese mitten crab (<i>Eriocheir sinensis</i>) varieties have had a negative tendency. Meanwhile, the status of wild germplasm resources of <i>E. sinensis</i> is unknown, hindering the utilization of wild germplasm resources and the green development of the <i>E. sinensis</i> industry. Thus, the conservation of the wild <i>E. sinensis</i> germplasm resource is of great significance. To this end, we collected wild <i>E. sinensis</i> from two different river basins, the Yangtze River basin, and the Liaohe River basin, and analyzed the genetic diversity as well as the genetic differentiation in <i>E. sinensis</i> populations. Based on eight microsatellite markers, we found moderate genetic diversity in <i>E. sinensis</i> populations regardless of river basin. Based on the mitochondrial D-loop region, we found that all populations are at mutation drift equilibrium, while the <i>Nm</i> between any two populations is greater than 1. We hypothesized the existence of island model gene flow patterns among <i>E. sinensis</i>. Interestingly, genetic differentiation among <i>E. sinensis</i> populations was low, except that between Liaohe and Anqing or Shanghai populations. Additionally, geometric morphological analysis could distinguish <i>E. sinensis</i> from different basins, with an accuracy of 94.2–100%. Given the similar genetic diversity in the two basins, the genetic convergence of <i>E. sinensis</i> from different basins deserves further attention.
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