Given the commercial and ecological importance of the dwindling Chesapeake Bay blue crab (Callinectes sapidus) population there is a surprising scarcity of information concerning the molecular ecology of this species. The few studies published to date are based on allozyme data and indicate a single, panmictic population along the Atlantic coast. To address this short-coming we have initiated the development of genetic markers from both the nuclear and mitochondrial genomes of the blue crab. Here we report the entire nucleotide sequence for the blue crab mitochondrial genome (mtDNA), which is a 16,263 bp in length, circular, and A+T-rich (69.1%). We have identified all of the normal complement of 37 genes (for 13 proteins, 22 tRNAs, and two rRNAs) plus a large (1434 bp), hypervariable putative control region that is 78.2% A+T. Gene order and arrangement is similar to other arthropods (e.g. Artemia) but dramatically different from the hermit crab. which has a unique gene order among arthropods. As in the mtDNA of the swimming crab, Portunus trituberculatus. trnH is located between the trnE and trnF genes, rather than at its primitive position upstream of nad5. Genetic variation is matrilineally inherited based on parent/offspring screening for nucleotide variation in the putative control region. (c) 2005 Elsevier B.V All rights reserved.