We examined microsporidia (1976-2014) in natural populations of blood-sucking Aedes mosquitoes of Western Siberia with the focus on their biodiversity and ecology. In total, we recorded 31 species of Culicidae family mosquitoes in Western Siberia; 22 species of them belong to the univoltine genus Aedes, producing one generation per year (spring). As it has been shown, microsporidians infect 13 mosquito species. In this study, we isolated 26 microsporidian species representing five genera (Amblyospora, Andreanna, Dimeiospora, Novothelohania, and Trichoctosporea) from mosquitoes; of them, the Amblyospora species were the most abundant. The majority of species display a high level of host specificity. Microsporidians are found in all types of aquatic habitats; however, the highest diversity of parasites was observed in mainland temporary ponds. During the period of study, the prevalence rates of microsporidians infecting Aedes mosquitoes varied from 0.05 to100%, with the maximal parasite prevalence during mass mosquito pupation and imago emergence (mid-May-beginning of June). Low parasite loads (0.05-6.5%) are characteristic of the last 20 years.