Sequences of the intergenic transcribed spacer regions and the 5.8S rRNA gene (455 nucleotides) of type strains or representative isolates of 23 species and subspecies either currently assigned to Aspergillus subgenus Circumdati section Flavi or other closely related sections, were analyzed. Parsimony analysis of sequence data indicated that species of Aspergillus section Flavi form distinct clades. The three main clades identified based on sequence data could also be distinguished based on colony color, and their ubiquinone systems. The ‘A. flavus’ clade includes species characterized with Q-10(H₂) as their main ubiquinone, conidial colors in shades of green, and dark sclerotia. The ‘A. tamarii’ clade involves species with ubiquinone system Q-10(H₂), and conidia in shades of olive to brown, while the ‘A. alliaceus’ clade consists of species with Q-10 ubiquinone system, and conidia in shades of ocher. The synnematous species A. coremiiformis was found to be closely related to species in the ‘A. tamarii’ clade. A. thomii and A. terricola var. americana were found to be related to the ‘A. flavus’ clade in spite of producing brownish colonies. Three species, A. nomius, A. avenaceus, and A. leporis were found to form separate lineages not closely related to any of the main clades identified. It is suggested that A. clavatoflavus and A. zonatus be excluded from Aspergillus section Flavi. Phylogenetic analysis of partial 26S rRNA gene sequences (564 nucleotides) supported our findings.