The green sunfish (Lepomis cyanellus) is a species of freshwater fish in the Centrarchidae family of order Perciformes, which is native to a wide area of North America. This species was introduced into China in 1998 and became one of the economically important freshwater species. In this study, we determined the complete mitochondrial genome sequence of L. cyanellus. The total length of L. cyanellus mitogenome is 16,485 bp, which consists of 13 protein-coding genes, 22 tRNA genes, 2 rRNA genes, and 1 control region (D-loop), with the genome organization and gene order being identical to that of the typical vertebrate. The overall base compositions of the heavy strand are 27.5% A, 26.2% T, 29.9% C, and 16.4% G, with an A + T content of 53.7%. The mitochondrial genome of L. cyanellus shared 86.8% sequence identity with that of Lepomis macrochirus. The sequence information presented here will be useful for evolutionary as well as population genetic studied.