The complete sequence of the mitochondrial genome of the Japanese snapping shrimp Alpheus japonicus Miers （Crustacea： Decapoda： Caridea） is presented here. A comparative analysis based on the currently available mitochondrial genomic data re- vealed many previously unknown characteristics of the mitochondrial genomes of caridean shrimps. The A. japonicus mito- chondrial genome is 16487 bp long and contains the typical set of 37 metazoan genes. The gene arrangements in the mito- chondrial genomes of four previously studied carideans （Macrobrachium rosenbergii, M. nipponense, M. lanchesteri and Halocaridina rubra） were found to be identical to the pancrustacean ground pattern; thus, it was considered that gene rear- rangements probably did not occur in the suborder Caridea. In the present study, a translocation of the trnE gene involving in- version was found in Alpheus mitochondrial genomes. This phenomenon has not been reported in any other crustacean mito- chondrial genome that has been studied so far; however, the translocation of one transfer RNA gene （trnP or trnT） was report- ed in the mitochondrial genome of Exopalaemon carinicauda. When the ratios of the nonsynonymous and synonymous sub- stitutions rates （Ka/Ks） for the 13 protein coding genes from two Alpheus species （A. japonicus and A. distinguendus） and three Macrobrachium species （M. rosenbergii, M. nipponense, M. lanchesteri） were calculated, the KaIKs values for all the protein coding genes in Alpheus and Macrobrachium mitochondrial genomes were found to be less than 1 （between 0.0048 and 0.2057）, indicating that a strong purification selection had occurred. The phylogenetic tree that was constructed based on the mitochondrial protein coding genes in the genomes of nine related species indicated that Palaemonidae and Alpheidae formed a monophyly and shared a statistically significant relationship, （Palaemonidae＋Alpheidae）＋Atyidae, at the family level.
