Three Fusarium species: F. graminearum, F. culmorum and F. cerealis were identified in laboratory cultures and in sporodochia from spikelets of scabby wheat. SCAR (sequence characterized amplified region) primers were used to identify Fusarium species and nivalenol (NIV) and deoxynivalenol (DON) chemotypes within species in laboratory cultures and field collected heads harvested in 2006. Results from PCR analyses confirmed preliminary identifications of species on the basis of examination of macroconidia under a light microscope and identification of cultures on agar media. NIV and DON (3Ac-DON and 15Ac-DON) chemotypes were identified using PCR assay. Among samples and isolates of F. graminearum, the 15Ac-DON chemotype dominated, and among those where F. culmorum was identified, the 3Ac-DON chemotype prevailed. Only 5 of the 41 isolates of F. graminearum tested, displayed the NIV chemotype. An increase in the frequency of F. graminearum and a decrease in the frequency of F. culmorum were found during 1998 to 2006.