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The complete sequence of mitochondrial DNA (mt DNA) from Stichopus sp. (Echinodermata: Holothuroidea: Stichopodidae: Stichopus) was acquired using conventional PCR and long PCR followed by cloning and sequencing. The mt DNA is a circular molecule of 16 257 bp in length, containing the set of 37 genes, including 13 protein-coding genes ( PCGs), 22 t RNA genes and two ribosomal RNA genes. The plus strand consists of 30.9% A, 23.7% C, 16.0% G and 29.3% T bases (AT skew = 0.027; GC skew = −0.194). All 13 PCGs encode a total of 3782 amino acids and all 22 t RNA genes were predicted to be capable of folding into a clover-leaf secondary structure. Intergenetic regions in the mitochondrial genome of Stichopus sp. contain 903 bp in total, with the largest continuous region (674 bp, AT% = 58.6) between t RNA-Thr and t RNA-Pro. Analysis of phylogenetic relationship of family Stichopodidae and genetic distances (species among the family Stichopodidae and species within Stichopus monotuberculatus group) based on the partial cox1 sequence demonstrates that Stichopus sp. from the South China Sea is a member of S. monotuberculatus complex. [ABSTRACT FROM AUTHOR]