Two series of pot experiments were carried out in 2000-2001. The experiment was established using the method of randomized blocks in 4 replications. The object of the experiment was Elena cultivar winter wheat in the reproduction phase protected chemically with fungicides: Amistar 250SC and Bravo 500SC and plant resistance stimulator: Bion 50WG with doses recommended by the producers. Water-treated plants were the control combination. After 48 hours, 10 days and 20 days, the number of the population of rhizosphere colonising bacteria: Bacillus, Azotobacter, Pseudomonas, Ca3(PO4)2 – hydrolysing bacteria and Actinom ycetales was analysed. Species composition and the number of fungal colonies were also monitored. The aim of the study was to determine changes occurring in bacterial and fungal populations colonising winter wheat rhizosphere after the application of chemical protection agents. The number of Bacillus rhizobacteria and the Ca3(PO4)2 – hydrolysing bacteria colonising plant root system, 48 hours after spraying with a plant resistance stimulator Bion 50WG was considerably lower than in the control combination. After 10 days, however, it was significantly higher than in the control combination. Bacteria representing the genera of Pseudomonas and Azotobacter were not sensitive to the application of chemical agents. The number of species of fungal populations colonising the rhizosphere of chemically protected winter wheat was fewer than in the control combinations. Additionally, chemical plant protection reduced the number of fungal populations representing the genera of Fusarium and Trichoderma, especially in the initial periods of the observation.