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<i>Fusarium</i> head blight (FHB) can lead to dramatic yield losses and mycotoxin contamination in small grain cereals in Canada. To assess the extent and severity of FHB in oat, samples collected from 168 commercial oat fields in the province of Manitoba, Canada, during 2016–2018 were analyzed for the occurrence of <i>Fusarium</i> head blight and associated mycotoxins. Through morphological and molecular analysis, <i>F. poae</i> was found to be the predominant <i>Fusarium</i> species affecting oat, followed by <i>F. graminearum</i>, <i>F. sporotrichioides</i>, <i>F. avenaceum</i>, and <i>F. culmorum</i>. Deoxynivalenol (DON) and nivalenol (NIV), type B trichothecenes, were the two most abundant <i>Fusarium</i> mycotoxins detected in oat. Beauvericin (BEA) was also frequently detected, though at lower concentrations. Close clustering of <i>F. poae</i> and NIV/BEA, <i>F. graminearum</i> and DON, and <i>F. sporotrichioides</i> and HT2/T2 (type A trichothecenes) was detected in the principal component analysis. Sampling location and crop rotation significantly impacted the concentrations of <i>Fusarium</i> mycotoxins in oat. A phylogenetic analysis of 95 <i>F. poae</i> strains from Manitoba was conducted using the concatenated nucleotide sequences of <i>Tef-1α</i>, <i>Tri1</i>, and <i>Tri8</i> genes. The results indicated that all <i>F. poae</i> strains belong to a monophyletic lineage. Four subgroups of <i>F. poae</i> strains were identified; however, no correlations were observed between the grouping of <i>F. poae</i> strains and sample locations/crop rotations.