The saddleback silver-biddy Gerres limbatus is distributed in Indo-West Pacific Oceans, and associated with shallow coastal marine waters and estuaries. In this study, the complete mitochondrial genome of G. limbatus was firstly documented, which is 16,730 bp in length, including 13 protein coding genes, 22 transfer RNA genes and 2 ribosomal RNA genes. The Maximum Likelihood phylogenetic tree revealed that G. erythrourus was placed as the sister group to G. limbatus.