Production of malting barley for the craft brewing supply chain is a new priority in New York with acreage expanding each year. Fungal diseases and grain contamination with trichothecene mycotoxins are major constraints in the production of malting barley in the state. Little is known about the mycoflora of malting barley grain in New York and especially about the spectrum of Fusarium species associated with grain and mycotoxin contamination, so research was conducted to establish baseline data on grain mycoflora and mycotoxin profiles. A total of 41 malting barley grain samples from 2018 and 2019 was collected from commercial producers and analyzed for fungal flora with a focus on Fusarium. Diversity incidence was higher in 2018, a drier production season than in 2019. Fusarium graminearum and Fusarium poae predominated in both years. Biomass of these two Fusarium species in malting barley grain was estimated with a Real-Time PCR approach. The finding of significant nivalenol (NIV) suggests that NIV as well as deoxynivalenol (DON) should be quantified in grain lots bound for malting.