Small subunit ribosomal RNA (SSU rRNA) gene sequences were analyzed for six species and four genera of microsporidia from mosquito hosts; Amblyospora stimuli (Aedes stimulans), Amblyospora californica (Culex tarsalis),Amblyospora sp. (Culex salinarius), Edhazardia aedis (Aedes aegypti), Culicosporella lunata (Culex pilosus), and Parathelohania anophelis (Anopheles quadrimaculatus), Comparison of these sequences to those of other microsporidia show that these sequences are longer with the SSU rRNA gene of E. aedis being the longest microsporidia sequenced to date (1447 base pairs), Parsimony, maximum likelihood, and distance methods produced identical trees, suggesting that the above microsporidian taxa, contrary to current classification schemes, form a monophyletic group. Relationships within this group are further supported by high bootstrap and decay analysis values. Based on the molecular analysis, P. anophelis is the most divergent species in this group of mosquito parasites. Amblyospora is paraphyletic with A. californica and Amblyospora sp,, forming a sister taxon to a clade composed of E. aedis and A. stimuli. Culicosproa/Edhazardia lunata comprises a sister taxon to the Amblyospora/Edhazardia clade. The pattern of host relationships on the tree provides preliminary evidence that the branching pattern seen here may indicate that host-parasite cospeciation is an important mechanism of evolution in this group. (C) 1998 Academic Press.