Sunflower (Helianthus annuus L.) production can be limited by several stem diseases. Among these, Phomopsis stem canker causes frequent yield reductions in Australia, Europe and North America. In the U.S., while Diaporthe helianthi was assumed to be the sole causal agent, Diaporthe gulyae was found to cause Phomopsis stem canker in Australia. In order to determine the causal agent in the U.S., 234 isolates were cultured from 275 infected sunflower stems collected from the Northern Great Plains. Phylogenetic analyses of the internal transcribed spacer region, elongation factor subunit 1-α, and actin gene sequences confirmed two species, D. helianthi and D. gulyae. Four methods were tested to assess the Phomopsis stem canker response using four D. helianthi isolates on sunflowers. Stem-wound method was adopted for subsequent experiments based on the recovery of D. helianthi and its correlation with disease severity at 14- d after inoculation. Aggressiveness of two Diaporthe species was determined in greenhouse and results suggest they did not vary significantly (p=0.0012) in their aggressiveness, except at 3-d after inoculation. Among the nine genotypes screened for resistance, USDA ‘PI 162784’ and ‘PI 219649’ were less susceptible to the two Diaporthe spp. Fusarium is commonly regarded a minor pathogen on sunflowers in most production regions of the world. A total of 110 Fusarium isolates were recovered from 1,637 stalks randomly sampled for stem diseases in the Northern Great Plains and identified to species level. Phylogenetic analyses of repetitive-sequence-based polymerase chain reaction fingerprints and the translation elongation factor 1-alpha gene revealed that Fusarium isolates from sunflowers represented clades of eight species; namely, F. graminearum, F. proliferatum, F. culmorum, F. avenaceum, F. oxysporum, F. acuminatum, F. sporotrichioides and F. equiseti. Pathogenicity studies of eight Fusarium spp. in the greenhouse suggests F. sporotrichioides and F. equiseti were most aggressive. The study comparing the aggressiveness of three Fusarium spp. and V. dahliae isolates representing six VCGs showed V. dahliae VCG4B and VCG2A were significantly more aggressive (p ≤ 0.05) than F. sporotrichioides, F. oxysporum and F. equiseti. The identification of Diaporthe spp. and Fusarium spp. on sunflowers has implications for breeding for resistance and disease management.