This is the opening paper in the special issue of Fungal Diversity, which collates the data on defining species. Defining and recognizing species has long been a controversial issue. Since Darwin's proposed origin of species, over 30 species criteria have been brought forth and used to define species boundaries. In recent times, phylogenetic analyses based on multiple loci have been extensively used as a method to define species boundaries. However, only a few mycologists are aware that phylogenetic species criteria can mask discordances among fungal groups, leading to inaccurately defined species boundaries. In the current review, we discuss species recognition criteria, how and where these criteria can be applied along with their limitations and derived alternatives. In order to delimit fungal species, authors need to take into account not only the phylogenetic and phenotypic coherence, but also the timing of events that lead to fungal speciation and subsequent diversifications. Variations in the rate of phenotypic diversifications and convergent fungal evolution make it difficult to establish a universal species recognition criterion. The best practice can only be defined in the context of each fungal group. In this review, we provide a set of guidelines, encouraging an integrative taxonomic approach for species delimitation that can be used to define fungal species boundaries in the future. The other papers in this special issue deal with fungal speciation in Ascomycota, Dothideomycetes , Basidiomycota , basal fungi, lichen-forming fungi, plant pathogenic fungi, and yeasts.