Pyrenophora teres f. maculata (Ptm) (spot form of net blotch) and Pyrenophora teres f. teres (Ptt) (net form of net blotch) are common leaf pathogens that cause net blotch disease of barley. From different regions of Turkey during the years 2012-2016 and 2017, 48 Ptt and 49 Ptm single spore isolates were obtained from different Hordeum species [H. vulgare (40 Ptm, 47 Ptt), H. spontaneum (7 Ptm, 1 Ptt) and H. bulbosum (2 Ptm)]. The genetic diversity of the isolates was accomplished using inter simple sequence repeat (ISSR) marker system. Using the species-specific and mating-type specific PCR primers, 48 Ptt and 49 Ptm isolates were identified as 30 MAT 1-1, 18 MAT1-2 and 27 MAT1-1, 22 MAT1-2 types, respectively. In order to determine genetic diversity of isolates, 10 ISSR primers were used and seven of these primers showed optimal band numbers and intensities. The most useful primers were UBC 825 and UBC 807 for Ptt population and UBC 825, UBC 807 and UBC 827 for Ptm population. The similarity rate of the Ptm isolates was found to be lower than that of Ptt isolates. There was no definite separation by year, mating type or geographical area. However, Ptt population was clustered more by location. The similarity rate of isolates obtained from wild barleys collected from Southeast Anatolia region of Turkey located in the Fertile Crescent region were low. Although some isolates from the same wild hosts and provinces showed low similarity, some isolates obtained from different wild hosts showed higher similarity to each other. This variation in isolates from wild barleys may contribute to the genetic diversity of the P. teres population. Genetic diversity of Ptt and Ptm populations in Turkey was assessed for the first time with this study. Investigation of pathogen biology and genetic structure will be useful for the development of disease control strategies.