Microbial pathogens were important in the evolution of insect societies and remain a major cause of colony death. The differential effects are reported of antimicrobial compounds extracted from six species of Australian native bees on the spores and hyphae of the entomopathogenic fungus Cordyceps bassiana. The bee species were: Amegilla bombiformis, A. asserta, Exoneura robusta, E. nigrescens, Exoneurella tridentata and Trigona carbonaria. The fungus was isolated from E. robusta and it was this species that showed the greatest activity against both Cordyceps spore germination and hyphal growth. One explanation is that anti-Cordyceps activity may have been under greatest selection in this bee species, but its congener, E. nigrescens, showed only slightly weaker activity against the pathogen. In contrast, A. bombiformis, A. asserta, E. tridentata and T. carbonaria showed considerable variation in anti-Cordyceps activity. Nevertheless, there was a trend of greater activity against Cordyceps spore germination than hyphal growth. On the basis of this result, a mechanism whereby fungal pathogens may have been important drivers of social evolution is suggested.