Abstract: Golden pompano (Trachinotus blochii) is an important marine aquaculture species in China, particularly within Hainan Province, which serves as a primary hub for pompano culture and seedling supply. In order to assess the genetic diversity and population structure of cultured golden pompano populations in Hainan Province, a population genetic analysis was conducted using 16 microsatellite markers on 210 individuals collected from three breeding companies situated in Hainan’s Dongfang base (referred as CH population), Lingshui base (referred as QL population), and Sanya base (referred as LL population). The results revealed a total of 251 alleles (N_a) detected across the 16 microsatellite markers in the three populations. The average observed heterozygosity (H_o), expected heterozygosity (H_e) and average polymorphic information content (PIC) were 0.630, 0.714, and 0.679, respectively. The average gene flow (N_m) across all loci was calculated as 5.217. Notably, the QL population showed higher genetic polymorphism. Nei’s genetic differentiation coefficient (F_st) among the populations ranged from 0.017 to 0.038. The AMOVA analysis revealed that 87% of the total genetic variation resided among individuals within populations. The STRUCTURE analysis clustered the populations into two subgroups (K=2), with QL and LL forming a genetic subgroup I, and CH forming genetic subgroup II. The UPGMA clustering analysis was consistent with the STRUCTURE results, and further revealed fine-scale genetic differentiation between the CH population and the QL and LL populations. Overall, cultured populations of golden pompano from different sources in Hainan province exhibited high genetic diversity, along with some level of genetic structure differences. These findings provide valuable data support for the evaluation and utilization of golden pompano genetic resources.