Polyphasic taxonomy has had a major impact on the species concept of the genus Aspergillus. New sibling species have been described that exhibit in vitro susceptibility profiles that differ significantly from that of Aspergillus fumigatus. While acquired resistance is an emerging problem in A. fumigatus, non-A. fumigatus Aspergillus species may be intrinsically resistant to specific classes of antifungal agents. Minimum inhibitory concentrations of amphotericin B and azoles for some of the non-A. fumigatus Aspergillus species are elevated compared to A. fumigatus. Furthermore, the clinical presentation and evolution of invasive infections caused by these species may differ from that commonly observed for A. fumigatus. As the role of the newly identified Aspergillus species in causing invasive aspergillosis remains unclear, surveillance networks that incorporate sequence-based identification of clinical isolates are needed to determine the species distribution, the clinical disease and outcome of patients with invasive aspergillosis. Preclinical and clinical studies are needed to further improve the methods for in vitro susceptibility testing and to investigate the impact of elevated MICs on antifungal drug efficacy.