Abstract: 【Objective】To provide reference for mating and pedigree analysis in the breeding plan that the species in this research group could adapt to Shanghai's unique climate, genetic information abundance and the degree of genetic differentiation among different Litopenaeus vannamei breeding populations were clarified.【Method】Thirteen pairs of microsatellite primers were used to analyze the genetic diversity of nine L. vannamei breeding populations, which came from two farms(Pesquera and San Alfonso) of the L. vannamei breeding company in Ecuador. It could also explore the richness of genetic information and differentiation among different populations.【Result】The number of alleles(Na) detected among nine L. vannamei breeding populations by 13 microsatellite loci ranged from 2 to 6, there were 37 alleles. Polymorphism information content index(PIC) was between 0.1292 and 0.6799, and the average PIC was 0.3326. Among the 13 microsatellite loci, only 1 microsatellite loci(TUMXLV9.116) had highly polymorphic, another 4 microsatellite loci(TUMXLV10.147, TUMXLV5.45c, TUMXLV10.191c and TUMXLV10.96) showed low polymorphism, and the remaining 8 microsatellite loci were moderately polymorphism. Otherwise, the observed heterozygosity(Ho) of 9 populations ranged from 0.2225 to 0.3662, and the average Ho was 0.2915. Expected heterozygosity(He) ranged from 0.3317 to 0.4539, and the average He was 0.3974. Hardy-Weinberg balance index(D) was ranging from 0.0214 to 0.4214. Among which the D of the San Alfonso P23 population and the Pesquera P23 population were relatively closer to 0, and their genotype distribution was close to the Hardy-Weinberg balance state. The numerical valueof mean differentiation index(F_st) was 0.1259, indicating that there was 12.59% of genetic differentiation took place between the populations, and 87.41% of genetic differentiation occurred within the populations. Besides, the mean gene flow(Nm) between populations was 1.7356, indicating that genetic drift had not been able to dominate the change of population genetic structure. Among the 9 L. vannamei breeding populations, the genetic distance between Pesquera 29 and Pesquera 15 was the largest(0.2426), and the genetic distance between San Alfonso 23 and Pesquera 23 was the smallest(0.0215). According to the UPGMA clustering based on genetic distance, the 9 L. vannamei populations could be divided into two major groups, among which the Pesquera 29 population and the San Alfonso 12 population were grouped independently into one group.【Conclusion】In the 9 breeding populations, lost observed allelic genes occurs, and they have low genetic diversity and moderate degree of differentiation among populations. It is possible to enrich the diversity of off spring populations by introducing populations from different regions with different genetic backgrounds and long genetic distance as parents.