In this study, the complete 16,184 bp mitochondrial genome of <i>Cyclograpsus intermedius</i> was determined from a specimen collected in South Korea. It consists of 13 protein-coding, 22 tRNA, 2 rRNA genes, and a non-coding A + T rich region. The base composition of the heavy strand in the mitochondrial genome was 34.7% A, 10.7% G, 18.7% C, and 35.9% T, resulting in a G + C content of 29.4%. A maximum-likelihood phylogenetic tree based on the 13 mitochondrial protein-coding genes showed that <i>C. intermedius</i> clustered together with the Varunidae. These molecular data will be useful for studying the evolutionary relationships among crab species.