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The complete mitochondrial genome of Colochirus quadrangularis was obtained and described in this study. This complete mitochondrial genome is 17,157 bp in length and consists of 13 protein-coding genes, 2 ribosomal RNA genes, and 22 transfer RNA genes. Except ND6 and 5 tRNAs, the others were encoded by the heavy strand. The overall base composition of the heavy-strand was 40.23% A, 11.31% G, 21.76% C, and 26.71% T, with a high G + C content of 33.07%. The phylogenetic analysis suggested that C. quadrangularis was closest to Cucumaria miniata. The newly described mitochondrial genome may provide valuable data for the phylogenetic analysis for Holothuroidea.