Members of Aspergillus section Fumigati are important animal pathogens and food contaminants. There is considerable variation among the 16 currently recognized species in this section, particularly in their mating systems: five are known to be strictly mitosporic, nine are homothallic, and two are heterothallic. Phylogenetic relationships were inferred among members of Aspergillus section Fumigati based on partial DNA sequences from the benA beta-tubulin and rodA hydrophobin genes. Aspergillus clavatus was chosen as an outgroup. The two gene regions provided nearly equal numbers of phylogenetically informative nucleotide characters. The rodA region possessed a considerably higher level of inferred amino acid variation than did the benA region. The results of a partition homogeneity test showed that the benA and rodA data sets were not in significant conflict, and the topologies of the most parsimonious trees for the two data sets differed only in branches that were not strongly supported by bootstrapping. The data sets in combination showed that morphological and secondary metabolite characters used in taxonomy were not strongly correlated with phylogeny. Mixed interrelationships were found among strictly mitotic, homothallic (selfing and outcrossing) and heterothallic (obligately outcrossing) taxa, suggesting multiple independent losses of the Neosartorya sexual state and possible derivation of heterothallism from homothallism through loss of self compatibility. The food spoiling species N. fischeri was identified as the closest known meiotic relative to the cosmopolitan species most often implicated in human aspergillosis, A. fumigatus.