The genetics and molecular biology of the commercially important Chinese spiny lobster, Panulirus stimpsoni are little known. Here, we present the complete mitochondrial genome sequence of P. stimpsoni, determined by the long polymerase chain reaction and primer walking sequencing method. The entire genome is 15,677 bp in length, encoding the standard set of 13 protein-coding genes, two ribosomal RNA genes, and 22 transfer RNA genes. The overall A+T content of the genome is 65.6%, lower than most malacostracan species. The gene order is consistent with the pancrustacean ground pattern. Several conserved elements were identified from P. stimpsoni control region, viz. one [TA(A)]n-block, two GA-blocks and three hairpin structures. However, the position of [TA(A)]n-block and number of hairpin structure are different from those in the congeneric P. japonicus and other decapods. Phylogenetic analyses using the concatenated nucleotide and amino acid sequences of 13 protein-coding genes do not support the monophyly of suborder Pleocyemata, which is in contrast to most morphological and molecular results. However, the position of Palinura and Astacidea is unstable, as represented by the basal or sister branches to other Reptantia species. P. stimpsoni, as the second species of Palinura with complete mitochondrial genome available, will provide important information on both genomics and conservation biology of the group.