Intermediate wheatgrass (Thinopyrum intermedium (Host) Barkworth & D. R. Dewey subsp. intermedium] (IWG), Kernza^®) is a promising perennial grain candidate that has the potential to provide food for humans as well as environmental services. In the long-term vision of growing IWG commercially, reliability of the plants to survive and persist against disease and pathogens is essential for its feasible use. Genomics may be used to efficiently increase disease resistant traits. We evaluated selections from The Land Institute’s (TLI) Cycle 7 breeding program from 2018-2020 with each cycle containing 460 Cycle 7 genets and 140 wheat and wheatgrass replicated checks to identify chromosomal regions associated with resistance to disease. Using genotyping-by-sequencing markers, quantitative trait loci (QTL) were mapped for 18 different disease and agronomic traits using genome-wide association analysis. Data was evaluated by-year which revealed 169 unique marker-trait associations (MTA) across 10 different traits. Two loci associated with fusarium head blight (FHB) resistance were significant across multiple years (p < 0.05). FHB and the mycotoxins produced are devastating to wheat production around the world. Significant loci for FHB related traits were also used to do a candidate gene search which provided potential resistance genes in this new grain. The identification of loci associated with disease resistance or tolerance may be useful in selecting more resistant IWG varieties for future development.