Plant pathogenic fungi from the genus Fusarium can cause economically important diseases of several different agricultural crops, including Fusarium Head Blight (FHB) of wheat. In addition to physically damaging the crops and causing reduced yield, these fungi produce toxins that contaminate the grains and make their products unsafe for consumption. Fungi causing this disease are considerably diverse in their biology with the most prominent and globally distributed species being from the F. graminearum species complex. Fungi from other taxonomic groups, such as F. avenaceum from the F. tricinctum species complex, also cause FHB and have the same geographical ranges as FHB pathogens from the F. graminearum species complex. This study explores the genomic similarities and differences between FHB fungi to: 1) better understand their diversity, and 2) identify genes that may be contributing to toxin production and disease. Whole genome sequencing and comparative genomics was performed on three species within the F. graminearum species complex; F. graminearum, F. meridionale, and F. asiaticum. Patterns of genomic and genetic variation were used to identify genomic regions and genes that are different between genomes. We then performed more detailed analyses of the biological interactions between two North American strains of F. graminearum that are from distinctly different genetic populations and produce different toxins. Our analyses indicated that one strain is more competitive than the other and that isolate-isolate interactions negatively impact toxin production and disease. We also identified a region of the genome that is highly variable between the two strains and when this region was compared to other strains of F. graminearum, the analyses indicated it is part of the accessory genome of the F. graminearum species and genus. Finally, we also performed whole genome sequencing and comparative genomics of three F. avenaceum isolates, which are FHB pathogens within the F. tricinctum species complex that are distantly related to the F. graminearum species complex. Our analyses indicated that the F. avenaceum genome is larger than that of F. graminearum and contains a different genetic repertoire that may contribute to toxin production and disease.