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Among marine species distributed in the Indian Ocean and the Pacific, the Indo–Pacific Barrier (IPB) has been found to be an important barrier of divergence of species distributed on both sides. Among the five species of the genus <i>Pampus</i>, only <i>Pampus chinensis</i> and <i>P. cinereus</i> are distributed across the western Pacific and the Indian Oceans and have not been studied comparatively using extensive sampling and gene markers. Furthermore, the origin and history of genus <i>Pampus</i> remain unrevealed. We used thousands of nuclear loci based on target gene enrichment to explore genetic structure of <i>P. chinensis</i> and <i>P. cinereus</i> across the western Pacific and Indian Oceans. We performed divergence dating and ancestral area reconstruction analysis and inferred the dispersal routes of the <i>Pampus</i> species. The results suggest that the IPB played an important role in the differentiation between populations among the two oceans for both <i>P. chinensis</i> and <i>P. cinereus</i>, dividing species into the Pacific lineage and the Indian Ocean lineage. Low sea level in the late Pleistocene may be the main cause. The result also showed that the South China Sea was the center of origin of the genus <i>Pampus</i>, and dispersal routes of each species may be associated with the ocean currents. Our study provided new examples for the IPB effect on marine species.