We reported the complete sequence of the mitochondrial (mt) genome of the deep-sea vent shrimp Alvinocaris chelys. This is the first complete mt genome obtained for the hydrothermal vent shrimp. The gene arrangement of the A. chelys mt genome is identical to the pancrustacean ground pattern as in most of the other caridean shrimp mt genomes available to date. However, there is an exceptionally long intergene spacer (86 bp in length) existed between the ND1 and tRNA(Leu)-CUN genes that is not previously reported. Our results provide further evidence that the mt gene order is highly conserved among caridean shrimp, in contrast to the other decapod infraorder such as Brachyura or Anomura which are of comparable or lower diversity.