One of the common causes of mass death in bee colonies is the infectious disease nosemosis, which is caused by two types of microsporidia, Nosema apis and Nosema ceranae. Of the many factors contributing to the spread of nosemosis, in this paper we consider the hybridization of subspecies of Apis mellifera L. In most of Russia, the native subspecies is the dark forest bee Apis mellifera mellifera, which is representative of the evolutionary lineage M. The export of bee packages and queens from the southern regions of Russia and other countries has led to the fragmentation of the range of these subspecies. First, we determined the maternal and paternal ancestry of 349 honey bee colonies across 12 beekeeping regions of Russia using the mitochondrial tRNAleu-COII locus and nine nuclear SSR markers (Ap243, 4a110, A024, A008, A43, A113, A088, Ap049, and A028). Among them, 140 colonies belonged to subspecies A. m. mellifera, 58 colonies were of hybrid origin, and 151 colonies belonged to evolutionary lineage C. Then, using microscopy and PCR analysis, we performed diagnostics of nosemosis in the studied colonies: N. apis was detected in 87 colonies, N. ceranae in 102 colonies, and coinfection was observed in 36 colonies. The results of our study indicate that the main reservoir of Nosema microsporidia was bees of evolutionary lineage C.