Abstract: We compared the genetic diversity and structure of cultivated population of Macrobrachium rosenbergii collected from different areas in China and Thailand by microsatellite analysis. Twelve fluorescently labeled primers were used to amplify microsatellite DNA from three Guangdong cultivated populations (GD1, GD2 and GD3), one Jiangsu cultivated population (JS) in China and two cultivated populations in Thailand (TG1 and TG2). The results show that the detected microsatellite loci possessed high polymorphism (PIC=0.853~0.941). All the populations analyzed displayed high genetic diversity (H_e=0.848~0.896). Genetic differentiation index (F_st) and AMOVA analysis reveal that the genetic differentiation within populations was relatively low (F_st < 0.15). About 5.27% genetic variation was derived from inter-populations, while 94.73% variation was derived from intra-population. Nei′s genetic distance indicates that the genetic distance between JS and GD2 population was the lowest (0.160 8), while that between the GD1 population and TG2 population was the highest (0.695 8). Phylogenetic analysis displays that these six M.rosenbergii populations could be divided into two groups. GD1, GD2, GD3 and JS populations were clustered together as one group and TG1 population was clustered with the TG2 population as another group. The results demonstrate that the analyzed cultivated M.rosenbergii populations maintained relatively high genetic diversity, and there was low kinship between China and Thailand populations.