Abstract: In order to explore the genetic diversity of the selective breeding population of Chinese mitten crab Eriocheir sinensis, 20 microsatellite markers were used to analyze the genetic diversity of 3 consecutive generations of strain A and strain B of “Changdang Lake 1” Chinese mitten crab. The results are presented in the following, a total of 551 alleles were detected from 20 microsatellite markers for 6 populations. The average number of alleles (N_a) were 27.55, the average number of effective alleles (N_e) was 13.61, the average observed heterozygosity (H_o) was 0.72, the average expected heterozygosity (H_e) was 0.90, the average Shannon information index (I) was 2.73, and the average polymorphic information content (PIC) was 0.89. In the process of breeding, PIC of strain A and strain B had a downward trend, and H_e and H_o of each population maintained a high level. The effective population size (N_e) in G1 and G2 of strain A were 72.7 and 111.8, and the Ne in G1 and G2 of strain B were 67.7 and 115.8, maintaining a high level. The Hardy-Weinber balance test showed that 72.5% of the data deviated from Hardy-Weinber balance, indicating that the genetic structure of the breeding population was relatively unstable. The genetic distance between G0 and G1 of strain A was 0.2455, and it increased to 0.2607 between G1 and G2. The genetic distance between G0 and G1 of strain B was 0.1736, and it increased to 0.1751 between G1 and G2. The genetic differentiation coefficients (F_st) ranged from 0.0026 to 0.0125, indicating that the genetic differentiations among populations was light. The results of molecular variance analysis (AMOVA) analysis showed that only 0.87% of the variation originated from different populations of “Changdang Lake 1”, while 99.13% variation occurred among individuals within the population. In conclusion, the genetic diversity and the effective population size were maintained high in each population of “Changdang Lake 1” Chinese mitten crab, but the genetic structure was unstable, so enough breeding parents and genetic diversity should be maintained to prevent inbreeding depression in the future breeding of “Changdang Lake 1”. This study may provide practical reference for the breeding of new strain of Chinese mitten crab, and accumulate data onto the continuous breeding and promotion of “Changdang Lake 1”.