The amplified fragment length polymorphism (AFLP) technique was used to study the genetic structure of Pyrenophora teres, the causal agent of barley net blotch disease. Samples were collected from five locations in Lithuania in 2008. All 145 isolates had unique AFLP patterns. Hierarchical analysis of molecular variance (AMOVA) detected most of the variation (86.9%) within a field population. No correlation was identified between the population pairwise fixation indices and the distance between the sampling locations. However, genetic differentiation (FST=0.131) among field populations was significant (P<0.001). The smallest percentage of variation (5.8%) was observed between isolates of different mating types within population, the genetic differentiation was low (Fsc=0.064, P<0.001). Multilocus association test showed that populations were in linkage disequilibrium, suggesting that reproduction occurs mainly asexually.