The genetic structure of different trituberculatus generations was analyzed based on microsatellite DNA markers. Sixteen microsatellite markers were used to analyze the genetic structure and genetic diversity of the selected populations of inbred Portunus rituberculatus from F1 to F4. The results showed that the genetic diversity of the breeding population was decreasing . The the average polymorphism information content (PIC) of the 16 microsatellite markers decreased from 0. 6753 to 0.4061, the average allele number from 3.5 to 2.1333, the average heterozygosity from 0.6435 to 0.4774 and the average rate of allele homozygous from 0.5669 to 0.4024. We tested all loci for H-W, there are different degrees of deviation from equilibrium in each generation. There are different degrees of genetic differentiation by F-test for each system, the results show that 19.07% of the genetic differentiation is among populations, 80.93% of the genetic differentiation is within the group. In addition, the Fis value calculations show that four families on the whole are expressed as a certain degree of heterozygosity, which F4 has 12 sites, F3 has six sites, F2 has three sites, F1, 8 loci in heterozygosity status.Increasing genetic distance, adjacent genetic similarity between generations gradually increased. With the breeding, the results show that after 4 consecutive generations of breeding.The genetic basis of breeding gradually purified homozygous and genotype gradually moving towards stable.We are expected to get more stable strains with further breeding.