To objectively assess the genetic diversity of Procambarus clarkii cultured populations in the vicinity of Nanning， Guangxi， three populations of P. clarkii from Nanning （AJ， LQ and SL）， and one population each from Jingzhou， Hubei （JZ） and Hukou， Jiangxi （HK） were collected. The level of genetic diversity was investigated using morphology and microsatellite markers. Morphological analysis showed that the total discrimination accuracy of female and male populations was 68.59% and 73.60%， respectively. Morphological clustering grouped the three Nanning populations into the same branch as the JZ population， indicating that the three Nanning populations had high morphological similarity. Microsatellite analysis revealed that the AJ population and LQ population had the highest genetic diversity， followed by the SL population and HK population. The genetic differentiation coefficient and genetic distance between the LQ population and SL population were the smallest. The results indicated that the populations of P. clarkii in Nanning， Guangxi had high genetic diversity， and that the introduction of P. clarkii from abroad or hybridization between different geographical populations may be an important way to enhance the genetic diversity of P. clarkii.