Areal of G. fasciatus in Baikal Lake is subdivided into four geographically continuous regions inhabited by four genetically distinct populations. Gene flow between the populations is impeded significantly. Geographic barriers between populations are absent. One of the potential reasons for that might be the ecological reproductive isolation caused by differential infection with microsporidia. We have found that indeed different populations differ dramatically both by species of microsporidian parasites and infection rate. This may point at the participation of the parasites in isolation of these populations and thereby in process of the speciation.