The small yellow croaker (Larimichthys polyactis) is one of the most commercially exploited marine fish species (Family: Sciaenidae) occurring along the coastal waters of northwestern Pacific. In this study, we employed next generation high-throughput DNA sequencing to characterize whole genome DNA sequence of L. polyactis via de novo assembly. The estimate of L. polyactis genome size is 649 Mb. A phylogeny based on single-copy ortholog sequences indicates that L. polyactis and L. crocea shared the closest affinity. Our results could guide sustainable fishery management of L. polyactis.