Objective: Fusarium spp. cause Fusarium head blight (FHB) and crown rot (CR) diseases. They also have harmful effects on animal and human health through their mycotoxins. Within the scope of this study, F. graminearum and F. culmorum isolates were purified from wheat ears and stalks contaminated with phytopathogens, which had been collected from various regions of Turkey, were identified and characterized by conventional and molecular methods. Materials and Methods: Sixty-eight Fusarium samples were isolated by single spore analysis and classified according to their macroconidia shape and size. Morphologically characterized samples were verified by amplification of SCAR markers. Their mating types (MAT) and chemotypes were also determined through polymerase chain reaction (PCR). Results: Thirty-eight F. graminearum and 30 F. culmorum isolates were identified via amplification of UBC85 and OPT18 SCAR markers, respectively. All isolates were determined as trichothecene producers by amplification of the tri5 gene. All F. graminarum isolates carry both MAT-1 and MAT-2 loci, whereas 7 of F. culmorum isolates were also determined as MAT-1 and 23 of them as MAT-2 mating types. Deoxynivalenol production capacity of all isolates was identified by tri13 amplification for chemotype determination. Conclusion: Routine monitoring of phytopathogens and their mycotoxin levels is a requirement since their annual levels may vary depending on environmental factors. This work provides knowledge about the distribution of Fusarium spp. leading to FHB and CR in different regions of Turkey between 2010 and 2020. Also, their chemotypes were demonstrated. Our studies will contribute to disease profiling and it is the first step in disease management.