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Pampus argenteus is a broadly exploited pelagic fish species, commonly misidentified as Pampus echinogaster. Genetic variation and population structure in Pampus argenteus was studied based on seven microsatellite loci. The observed high average allele number, heterozygosity values, and polymorphism information content of P. argenteus suggested high genetic diversity. No population genetic differentiation was detected based on the results of pairwise Fst, three-dimensional factorial correspondence analysis (3D-FCA) and STRUCTURE analysis, which implied continuous gene flow. Wilcoxon signed rank tests did not indicate significant heterozygosity excess, and recent genetic bottleneck events were not detected. Coupled with previous mitochondrial DNA results, the findings presented here indicate that high gene flow characterizes the current phylogeographic pattern of the species.