We determined the complete mitochondrial DNA sequence for a swimming crab Portunus trituberculatus (Miers, 1876) (Crustacea: Decapoda: Brachyura). The entire genome was amplified using a long PCR technique, and the products were subsequently used as templates for direct sequencing using a primer walking strategy. The genome (16,026 bp) contained the same 37 genes (two rRNAs, 22 tRNAs, and 13 proteins) plus the putative control region as found in other arthropods. The gene order of P. trituberculatus was largely identical to those so far obtained for other arthropods such as Drosophila yakuba, although the relative position of the tRNA(His) gene differed from all other arthropods studied so far. While the tRNA(His) gene in other arthropod mitochondrial genomes is located between the ND4 and ND5 genes, that of P. trituberculatus was found between the tRNA(Glu) and the tRNA(Phe) genes, which were located downstream of the ND5 gene. The present gene order could have resulted from tandem duplication occurring in the tRNA(Phe)-ND5-tRNA(His) region (typical gene order in other arthropods) and following deletions of redundant genes. This is the first report of a mitochondrial genome of a brachyuran crab, one of the most diversified and economically important groups of crustaceans.