Mitochondrial genomes (mitogenomes) of two hydrothermal vent crustaceans have been completely sequenced and analyzed. Metazoan mitogenomes usually consist of the same 37 genes, which contain useful information for phylogenetic analyses and evolution modeling. Although complete mitogenomes have been detertermined for over 1000 animals to date, hydrothermal vent species have, thus far, remained excluded due to the scarcity of collected specimens. The mitogenome of the vent galatheid crab Shinkaia crosnieri is 15182 bp in length and is composed of the same genes as others except for four tRNA genes missing. A mechanism of cytoplasmic tRNA import was addressed to compensate for the absent tRNAs. A non-coding control region of 327 bp was discovered, which was the smallest one within decapods so far. The genome exhibits a novel arrangement of mitochondrial genes. At least six rearrangements happned successively derived from the ancestral pancrustacean (crustacean+hexapod) pattern depicted by the Macrobrachium rosenbergii mitogenome. Phylogenetic analyes place S. crosnieri as a close relative of the hermit crab Pagurus longicarpus. The mitogenome of the vent bythograeid crab Austinograea yunohana is a 15567-bp circular molecule. The arrangement of the genome is identical to the other four brachyuran mitogenomes. The putative control region of A. yunohana is the most similar to that of the Australian giant crab Pseudocarcinus gigas. The phylogenetic analyses also confirm the nearest relationships between A. yunohana and P. gigas. The results indicate that the closely related species often exhibit identical mitogenome arrangements. In genetic contents, both mitogenomes of S. crosnieri and A. yunohana show no substantial difference with their non-vent counterparts, providing important evidence for the extinction/repopulation hypothesis of the origins of the hydrothermal vent species.On the other hand, CLOCK, which belongs to the basic helix-loop-helix (bHLH)/PER-ARNT-SIM (PAS) superfamily of transcription factors, is one of the most essential proteins involved in circadian systems of animals. Clock genes have been cloned from mammals, insects, birds, fish, and amphibians. In the present study, a Clock homolog (termed Mar-Clock) was successfully isolated from the giant prawn, Macrobrachium rosenbergii. The 2949-bp cDNA contained a 2115-bp open reading frame that encoded a putative CLOCK protein of 704 amino acids (termed Mar-CLOCK) exhibiting high identities with other CLOCKs (30-35%). This is the first report of a circadian clock gene from crustaceans. Mar-CLOCK possesses an exceptionally long glutamine-rich domain (140 amino acids) in its C-terminus and is supposed to function in transcriptional activation. It was observed that Mar-Clock was expressed in all tested tissues. Semiquantitative RT-PCR was performed to investigate the gene expression profile during the light-dark cycle. The results indicated that the expression of the Mar-Clock gene had no significant rhythmicity in central nervous tissues or peripheral tissues. Furthermore, gene expression tended to increase in the central nervous system of eyestalk-ablated or constant dark (DD) prawns. These results will provide important information for researches on circadian clocks of vent crustaceans that live under constant-dark environments and lose their eyestalks.