Abstract: In this study, the SSR markers of Macrobrachium rosenbergii were excavated by transcriptome sequencing, and 18592 SSR loci were obtained. 63 SSR loci were selected and 10 individuals were utilized to screen the polymorphic loci, and 31 SSR markers with polymorphism were obtained finally. Among which, 19 SSR markers were used to analyze the population genetic structure of 119 shrimps from the full-sib family group (FS) and 199 shrimps from the F3 wild group of Bangladesh (MJL), and the correlation between SSR loci and body mass traits was analyzed. The results showed that 40 alleles were detected in FS population, with an average alleles number of 2.1053, an average observed heterozygosity of 0.4525, an average expected heterozygosity of 0.3804, an average polymorphism information content of 0.3076, which was moderate genetic polymorphism; A total of 65 alleles were detected in MJL population, with an average alleles number of 3.4211, an average observed heterozygosity of 0.4105, an average expected heterozygosity of 0.4496, and an average polymorphism information content of 0.3882, which was also moderate genetic polymorphism. There was no correlation between 19 SSR loci and body weight in FS population (P>0.05), but 4 SSR loci were significantly correlated with body weight in MJL population (P<0.05). For the loci with significant differences, body weight traits of different genotypes were analyzed by multiple comparison, which showed that the mean body weight of MR28 277/285 genotype was significantly higher than that of 277/289 and 285/285 genotypes (P<0.01), and significantly higher than that of 285/289, 273/289, 270/273 and 285/293 genotypes (P<0.05); The mean body mass of genotypes 266/266 and 266/270 at MR32 was significantly higher than that of genotypes 270/270 (P<0.05) . The mean body mass of genotypes of 210/214 at MR34 was significantly higher than that of genotypes 210/210 and 214/214 (P<0.05). The mean body mass of genotypes of 174/190 at MR45 was significantly higher than that of genotypes 182/182 and 182/190 (P<0.05). The results lay a foundation for marker-assisted breeding of M. rosenbergii.