Human pathogenic aspergilli are identified in the clinical diagnostic laboratory predominantly by macro- and micro-morphology. Such phenotypic characteristics are largely subjective and unstable, as they are influenced by environmental factors, including media and temperature of incubation. Recent advances in molecular biology have impacted the field of mycology; multiple studies have noted new genetically distinct species that are not easily distinguished by phenotypic characteristics. Strengths of molecular typing methods include objectivity and the ability to identify nonsporulating or slowly growing fungi. As such, molecular methods provide powerful tools for the study of the epidemiology, evolution and population biology of fungal pathogens. This review focuses on current and future methods of identifying aspergilli, and implications regarding Aspergillus species/strain identification.