The Chinese shad (Ilisha elongata) is economically import along the coast of the Northwest Pacific. The fisheries resource of the Chinese shad is declining in recent years, but its fine population structure has not been studied using genomic data and cryptic diversity may exist for this species. Understanding its population dynamics and diversity using genomic data is essential to better conservation and utilization of this species. A high-quality genome assembly of the Chinese shad also can provide useful resources for comparative study on evolution of interesting traits among coastal fishes, such as migration, fatty acid synthesis, intermuscular bones, etc.