Septoria Leaf Blotch caused by Zymoseptoria tritici is a major disease of wheat affecting many wheat-growing regions in the world. This study is the first to describe characteristics of the pathotype structure of Z. tritici isolates in Central Anatolia, Turkey, and to determine effective resistance genes for use in breeding strategies of Septoria Leaf Blotch Disease. Sixty isolates of Z. tritici were obtained from four intensive wheat production provinces during 2015 and 2017. The pathotypes were determined using a differential set that included 12 wheat genotypes. Twenty-eight pathotypes were identified, and Pathotype 1 prevailed in all areas investigated. The K-5 isolate from Konya province had the highest virulence on the differential genotypes and was characterized as Pathotype 28. Thirty-nine of the isolates were virulent on the resistance gene Stb-10, and all isolates were avirulent for the resistance gene Stb-6. It appears that resistance genes Stb-6 and Stb-12 could be used in breeding new varieties against Septoria Leaf Blotch Disease.