The parasitic nasal mite Ptilonyssus sairae Castro has been classified as one species, but we find that significant sequence divergence exists between host-specific mite populations. The low level of gene flow between conspecifics is probably a result of the parasites' low rate of dispersal among different bird host species. The internal transcribed spacer (ITS) of the nuclear ribosomal RNA gene from P. sairae populations was sequenced and used for phylogenetic inference and subsequently compared to their passerine bird host phylogeny. In addition to finding restricted gene flow between host-associated parasites, the reconciliation of host and parasite gene trees reveals statistically significant levels of strict cospeciation between bird hosts and host-specific mite populations. Our findings suggest that cryptic speciation may be common in this group of mites.