An exact micro-plot experiment was conducted to determine the effect of fungicides (treatments: Sandofan Manco 64 WP, Penncozeb 80 WP, Tanos 50 WG; Tanos 50 WG applied three times; Tanos 50 WG, Penncozeb 80 WP, Tanos 50 WG) on the severity of late blight and early blight in three potato cultivars and on the composition of fugal communities colonizing potato leaves. The tested fungicides significantly reduced the intensity of late blight and early blight. The efficacy of fungicidal control was affected by weather conditions and potato cultivars. The highest efficacy (30–36%) against late blight and early blight was noted in potato plants cv. Aster sprayed with Sandofan Manco 75 WG, Penncozeb 80 WP, Tanos 50 WG and Tanos 50 WG applied three times in the first year of the study. Sandofan Manco 75 WG, Penncozeb 80 WP, Tanos 50 WG, and Tanos 50 WG and Penncozeb WP 80 used alternately during the last two last growing seasons were most effective in late blight control in potato cv. Tara and Salto. In these cultivars, early blight was best controlled with Tanos 50 WG applied three times, and Tanos 50 WG and Penncozeb 80 WP used alternately. The lowest counts of Alternaria spp. – the causal agent of early blight – were isolated from potato leaves in the above treatments.