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Coilia brachygnathus is the only one freshwater fish of the genus Coilia in China. In this study, we determined the complete mitochondrial genome of Coilia brachygnathus from Chaohu Lake. It is 16,896 bp in length and consists of 13 protein-coding genes, 2 rRNA genes, 22 transfer RNA genes as well as a control region (CR). Over base composition of the mitogenome is A(31.2%), C(27.0%), T(26.3%), and G(15.5%), respectively. Phylogenetic analysis confirmed the evolutionary relatedness of C. brachygnathus to other fishes of genus Coilia and also revealed the phylogenetic relationship of this genus within Engraulidae at molecular levels.