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Deep-sea organisms survive in an extremely harsh environment. There must be some genetic adaptation mechanisms for them. We systematically characterized and compared the complete mitochondrial genome (mitogenome) of a deep-sea crab ( Chaceon granulates ) with those of shallow crabs. The mitogenome of the crab was 16126 bp in length, and encoded 37 genes as most of a metazoan mitogenome, including 13 protein-coding genes (PCGs), 22 transfer RNA ( tRNA ) genes, and 2 ribosomal RNA ( rRNA ) genes. The gene arrangement and orientation was conserved in the crabs. However, a unique mitogenome element regulator, the origin of light-strand replication (O L ), was firstly predicted in the present crab mitogenome. In addition, further positive selection analysis showed that two residues (33S in ND3 and 502I in ND5 ) in C. granulates mitogenome were positively selected, indicated the selective evolution of the deep-sea crab. Therefore, the mitogenome of deep-sea C. granulates showed a unique O L element and positive selection. These special features would influence the mitochondrial energy metabolism, and be involved in the adaptation of deep-sea environment, such as oxygen deficits and low temperatures.