The ridgetail white prawn (Exopalaemon carinicauda) is an important small to medium-sized economic species. Due to its strong reproductive capacity, fast growth, and excellent environmental adaptability, it has gradually become the main species for the development of saltwater aquaculture modes in China. However, like many aquaculture industries, robust genetic foundations are essential to ensure the growth and economic performance of breeding stock. It is necessary to continuously monitor the genetic variation in broodstock to maintain long-term sustainability. Eleven polymorphic microsatellite loci were used to analyze the genetic diversity and genetic differentiation of four consecutive generations (GP2–GP5) of an E. carinicauda breeding stock from 2021 to 2023 to reveal the genetic variation of different generations under low-salinity culture conditions. The results were as follows. A total of 11 microsatellite loci were amplified, and 70 alleles were detected, with fragment lengths ranging from 138 to 296 bp, of which 10 loci were moderately to highly polymorphic. The average observed heterozygosity (H_o) of GP2–GP5 breeding stock was 0.504, 0.555, 0.499, and 0.416, respectively; the average expected heterozygosity (H_e) was 0.564, 0.546, 0.554, and 0.550, respectively; and the average polymorphic information content (PIC) was 0.518, 0.483, 0.489, and 0.490, respectively. The genetic diversity of white shrimp slightly declined with successive generations of breeding but remained at a moderate level. Genetic differentiation results indicated that the degree of genetic differentiation between adjacent generations gradually increased from GP2 to GP5, showing weak differentiation. Additionally, the sufficient genetic exchange (N_m=11.32–14.62) between adjacent generations of the breeding stock gradually decreased. Cluster analysis also showed differences in genetic composition between generations, with the optimal K value being 2. The effective population size of E. carinicauda in different generations ranged from 3.1 to 37.1 individuals, and inbreeding within the stock was detected (F_is=0.061–0.212). This study illustrated that although the genetic diversity of the second to fifth generations of E. carinicauda remained relatively rich under low-salilnity culture conditions, it slightly declined over several generations. However, the species still showed good breeding potential. The stock exhibits weaker genetic differentiation and unstable structure, necessitating continuous monitoring and reinforcement. In future breeding efforts, it is crucial to prevent a reduction in effective population size to avoid issues such as inbreeding within the stock. The results of this study provide genetic data essential for the next step in developing a breeding plan for new low-salilnity-tolerant white shrimp varieties.