By using thirteen moderate and high polymorphic microsatellite DNA loci, this paper analyzed the genetic structure of wild Macrobrachium nipponense populations in Anhui section of Huaihe River. For the 11 M. nipponense populations, there were 118 loci presenting heterozygosity deficiency and obvious deviation from HardyWeinberg equilibrium after Bonferroni correction. The mean expected heterozygosity values of the 11 populations were all below 0.658, displaying a low genetic diversity, while higher genetic diversity appeared in WB and JG populations, and lower in GT populations. The 11 populations departed from mutationdrift equilibrium, suggesting that the population structure had experienced bottleneck effect and the population amount had declined. The AMOVA analysis across all the populations showed that the genetic divergence among the 11 populations was at a lower level (F_ST = 0.0116). 98.84 % of the genetic variation came from intrapopulation, and 1.16 % came from interpopulation, suggesting that all the M. nipponense populations in Anhui section of Huaihe River could be protected and managed as a single unit, which provides basic material for development and utilization of germplasm resonrces of M. nipponense.