The research presented in this thesis treats the taxonomic status of Alternaria and related genera with a further focus on the large-spored Alternaria species in section Porri and the small-spored Alternaria species in section Alternaria. Section Porri is the largest Alternaria section with regards to the number of species, and includes several important plant pathogens. The most commonly reported species in literature and type species of the genus Alternaria, Alternaria alternata, resides in section Alternaria. As A. alternata is considered as one of the most prolific producers of fungal allergens and is reported as pathogen on over 100 host plants, correct species identification is of utmost importance. In addition to the phylogenetic studies, genome and transcriptome sequence data were analysed to identify candidate loci for species identification within the small-spored Alternaria species, and microsatellite markers were used to study the genetic diversity and distribution of indoor Alternaria isolates in the USA. For end-users, the phylogenies and classifications presented in this thesis result in a more stable and understandable taxonomy and nomenclature of Alternaria and allied genera. This revised taxonomy will serve as a starting point for applied research performed by plant pathologist, breeders and medical mycologists in the field.