Overcrowding is a significant factor contributing to endemic infection with Sarcoptes scabiei in human and animal populations. However, since scabies mites from different host species are indistinguishable morphologically, it is unclear whether people can be infected from scabies-infested animals. Molecular fingerprinting was done using three S. scabiei-specific single locus hypervariable microsatellite markers, with a combined total of 70 known alleles. Multilocus analysis of 712 scabies mites from human and dog hosts in Ohio, Panama and Aboriginal communities in northern Australia now shows that genotypes of dog-derived and human-derived scabies cluster by host species rather than by geographic location. Because of the apparent genetic separation between human scabies and dog scabies, control programs for human scabies in endemic areas do not require resources directed against zoonotic infection from dogs.