Shrimp of the family Atyidae are important members of nearly all tropical (and most temperate) fresh and brackish water ecosystems in the world. To date, a complete mitochondrial genome from this important crustacean group has not been reported. Here, we present the complete mitochondrial DNA sequence of the Hawaiian atyid Halocaridina rubra [Holthuis, L.B., 1963. On red coloured shrimps (Decapoda, Caridea) from tropical land-locked saltwater pools. Zool. Meded.16, 261-279.] (Crustacea: Decapoda: Atyidae). The genome is a circular molecule of 16,065 bp and encodes the 37 mitochondrial genes (13 protein-coding, 22 tRNAs, and two rRNAs) typically found in the metazoa. Gene order and orientation in the H. rubra mitochondrial genome is syntenic with most malacostracans that have been examined to date. Of special note is the absence of the dihydrouridine (DHU) arm stem from tRNA(Tyr) and the use of CCG as an initiation codon for cytochrome oxidase subunit I (COI); these represent the first reported examples of such phenomena in the Malacostraca. Phylogenetic analyses utilizing complete mitochondrial sequences from other malacostracans place H. rubra as sister to Macrobrachium rosenbergii, which also belongs to the Infraorder Caridea. However, the placement of this infraorder, as well as the Infraorder Dendrobrachiata, in the phylogeny of the Decapoda varied depending on outgroup selection. Data from additional mitochondrial genomes, such as basal decapods like the Stenopodidea, should contribute to a better overall understanding of decapod phylogenetics.