Abstract: Eight pairs of primers were selected to analyze the genetic diversity of five random broodstock populations (ZA1, HN, ZA2, ZP and DS) of Litopenaeus vannamei by using microsatellite labeling technology. The results indicated that a total of seventy-five alleles (Na=75) were detected with eight pairs of primers in five populations, with average numbers of alleles as Na=3.875~7.000, average effective numbers of alleles as Ne=2.632~3.719 and average polymorphism information content as PIC=0.498~0.624. The average observed heterozygosity（Ho）was 0.410 to 0.562 and the average expected heterozygosity（He）was 0.589 to 0.687. The average number of inbreeding coefficient (Fis) of each population was 0.147~0.305, indicating a high degree of inbreeding in each population and the absence of heterozygotes. Except population ZP and DS, other groups deviated from equilibrium significantly at multiple microsatellite sites (P＜0.05), which indicated that most groups had the phenomenon of heterozygote deficiency. Genetic variation analysis results showed that the genetic differentiation index（Fst）was 0.028~0.199. According to Fst calculation, the genetic distance of Slatkin's was between 0.029 and 0.249. The results of this study showed that there were a different level of inbreeding phenomenon in the five broodstock populations of L. vannamei. In this paper, the genetic diversity of five broodstock populations of L. vannamei in xiamen was analyzed in order to clarify genetic structure, germplasm resources and inbreeding degree of broodstock populations of L. vannamei in Xiamen and provide background information and suggestions for purification, optimal protection, rejuvenation and genetic breeding of germplasm resources of L. vannamei for this area.