is a commercially important aquaculture species in China. was determined using inter-simple sequence repeat (ISSR) markers. The five populations were collected from Tai Lake of Jiangsu Province, Poyang Lake of Jiangxi Province, Nanman River of Yunnan Province, Yangtze River of Hubei Province and Botengsi Lake of Xinjiang Uygur Autonomous Region. A total of 142 bands were produced from 60 individuals by nine ISSR primers. At species level, the percentage of polymorphic loci (PPL), observed number of alles per locus (e), Nei’s gene diversity index() were 97.18%, 1.972, 0.312, 0.120 and . At population level, the percentage of polymorphism loci (PPL) varied greatly among populations, ranging from 29.58% to 61.97%. The ranged from 1.296 to 1.620, the effective number of alleles varied from 1.165 to 1.281. Nei’s gene diversity ranged from 0.098 to 0.172. Shannon’s information index with an average of 0.135 at the population level (). The total genetic diversity (s) were 0.201 and 0.135. The coefficient of genetic differentiation between populations () was 0.327 as estimated by partitioning of the total gene diversity (0.201). Population Nanchang exhibits great level of variability (PPL: 61.97%, I: 0.267), whereas the population HB exhibits the lowest level of variability (PPL: 29.58%, I: 0.147). Compared with other populations, Xinjiang population and Jiangsu population were genetically most similar (: 0.1923, D: 0.0542), while Xinjiang population and Yunnan population were most dissimilar (: 0.5950, D: 0.1559). The result of this study may be useful for the conservation and utilization of wild genetic resource of oriental river prawn.