Little yellow croaker (Larimichthys polyactis, L. polyactis) due to their special patterns of gonadal development become a good model for study formation of hermaphrodite. On the other hand, as the most famous commercial fishes in east Asia, the origin and evolution of L. polyactis and Larimichthys crocea are unclear. Here we report the genome sequence of the little yellow croaker, covering ~706 Mb (contig N50 and scaffold N50 are 1.21Mb and 4.52Mb, respectivly) with 25,233 protein-coding genes.