The species structure of plant parasitic nematode populations from the rhizosphere of winter wheat grown with crop rotation or in 48-year-old monoculture was analyzed and compared. Dominating species: Bitylenchus dubius, Merlinius microdorus, Paratylenchus neglectus and Heterodera avenae, in monoculture plots, had higher populations than in crop rotation plots. Heterodera avenae eggs and larvae were infected by pathogenic fungi in 68% of the monoculture crops (vs. 65–66% of the cysts from crop rotation), 12–20% of Paratylenchus sp. specimens were colonized by bacteria, mainly by Bacillus penetrans. This study shows nematological changes occurring in long-term wheat breeding, thus providing additional information necessary to fight dangerous viral vectors of the examined cereal.