Epigenetics is an emerging field in the regulation of biological processes in fungi. This study examines the role of one such epigenetic mechanism, DNA methylation, in development and pathogenicity of the fungal phytopathogen Fusarium graminearum. Two DNA methyltransferase genes were identified, and disruption of these genes resulted in growth, reproduction and pathogenicity related phenotypes. Deletion mutants displayed changes in growth, and were impaired in their ability to produce ascospores and infect susceptible wheat. Secondary metabolism was also affected, including deoxynivalenol toxin production, pigmentation, and the expression of novel unknown metabolites. Bisulfite sequencing resulted in the first DNA methylome of any Fusarium species, and analysis indicated DNA methylation is present on 0.1% of genomic cytosines, consistent with related fungi. Methylation sites were identified in genes related to cellular processes including development and pathogenicity. Altogether, our analysis shed light on the important epigenetic process of DNA methylation in a fungal plant pathogen.