Six flax cultivars (Linum usitatissimum L.) were evaluated for powdery mildew resistance in outdoor experience. Cultivars wilden, Bombay and Dakota were resistant (disease severity was 62.80, 58.77 and 69.70% respectively), while cultivars Cortland, sofie, and C.I. 2008 were susceptible (disease severity was 98.10, 97.90, and 87.07% respectively). DNA was extracted from cultivar leaves and subjected to random amplified polymorphic DNA (RAPD) analysis by using five random primers. Primer no.5 was partially successful in differentiating between susceptible cultivars sofie and C.I.2008 and the other resistant cultivars. Extracted DNA was subjected to inter – simple sequence repeat (ISSR) by using five random primers. Primer no.9 was successful in differentiating between the resistant cultivars and the susceptible ones. Primers no. 7 and no. 10 were partially successful in differentiation between some susceptible and resistant cultivars.