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The mitochondrial genome (mitogenome) provides important information for phylogenetic analysis and understanding evolutionary origins. Herein, we sequenced, annotated, and characterized the mitogenome of Metaplax longipes to better understand its molecular evolution and phylogeny. The 16,424 bp mitogenome includes 13 protein-coding genes (PCGs), 22 transfer RNA (tRNA) genes, two ribosomal RNA (rRNA) genes, and one control region. The length of control region is 1036 bp. The nucleotide composition of M. longipes is A + T: 71.7%, with a strong AT bias. Phylogenetic analysis shows that M. longipes is closely related to Cyclograpsus granulosus and Helice wuana, which belong to the same family Varunidae.