This study presents a revised method for the extraction of mitochondrial genome (mtDNA) from crayfish species of aquacultural interest, Pacifastacus leniusculus. The mean size of the mitochondrial genome is approximately 18,000 bp. Restriction fragment length polymorphism (RFLP) analysis performed on the mtDNA has revealed extensive genetic variability within this species. The estimated percentage of nucleotide sequence divergence among the four haplotypes found for P. leniusculus ranges from 1.16 to 3.99%. These data suggest that RFLP analysis of mtDNA may provide greater resolution than protein electrophoresis for population identification among signal crayfish populations. This marker offers new avenues for aquaculture and for understanding the genetic structure and evolutionary history of crayfish populations.