Project description:In this study, we firstly obtained the complete mitochondrial genome DNA sequence of the Ambassis gymnocephalus. Its length is 17,388?bp, containing 13 protein-coding genes, 2 rRNAs, 22 tRNAs and a large noncoding region. The overall length of protein coding genes is 11,448?bp, including A (26.75%), G (15.20%), T (26.44%) and C (31.61%). The A?+?T content of control region (1555?bp) is 60.45%. The protein-coding gene COI is started by GTG and ended by AGA. From the phylogenetic tree, we find A. gymnocephalus and Oreochromis niloticus has the closest relationship among 21 related species. This work will provide some valuable information for further studies on A. gymnocephalus and the family Ambassidae.