Psoroptic sheep scab and psoroptic otoacariasis of domestic rabbits occur in the same geographical regions of Switzerland. To address the question as to whether Psoroptes mites are naturally transmitted between sheep and rabbits, we determined the sequences of the rDNA second internal transcribed spacer (ITS-2) from psoroptic mites from sheep (5 field isolates from Switzerland and 2 laboratory isolates from Ireland and the UK) and from rabbits (8 field isolates from Switzerland). The ITS-2 sequences for all Psoroptes mites originating from sheep were identical and differed at 1 nucleotide position from all the sequences of the rabbit-derived isolates. A statistically significant difference between a rabbit-derived isolate and isolates originating from sheep was also obtained by morphometric analysis of the lengths of the outer opisthosomal setae. For comparative purposes, the ITS-2 sequences from Chorioptes and Sarcoptes collected in Switzerland were also determined. No intraspecies variation was found in 6 sarcoptic isolates from red foxes, with a sequence identity of 41% as compared to Psoroptes. The ITS-2 sequences of 3 chorioptic isolates differed by 24–29% from the Psoroptes sequence. Identical sequences were found for the Chorioptes isolates from sheep and a camel, which differed by 18% from the sequence of an isolate from a cow. These genetic data of psoroptic mites originating from sheep and rabbits from the same geographical area suggest the existence of epidemiologically separated populations.