Scientific names are crucial for communicating knowledge concerning fungi and fungus-like organisms. In plant pathology, they link information regarding biology, host range, distribution and potential risk to agriculture and food security. In the past, delimitation among pathogenic taxa was primarily based on morphological characteristics. Due to distinct species sharing overlapping characteristics, the morphological identification of species is often neither straightforward nor reliable. Hence, the phylogenetic species concept based on molecular phylogenetic reconstructions gained importance. The present opinion discusses what a fungal species is and how identification of species in plant pathology has changed over the past decades. In this context, host-specialization and species complexes are discussed. Furthermore, species concepts in plant pathology are examined using case studies from Bipolaris, Colletotrichum, Curvularia, Diaporthe, Diplodia, Meliola, Plasmopara, rust fungi and Trichoderma. Each entry contains a brief introduction to the genus, concepts used in species identification so far and the problems in describing a species followed by recommendations. The importance of correctly naming and identifying a species is addressed in the context of recent introductions, and we also discuss whether the introduction of new species in pathogenic genera has been overestimated. We also provide guidelines to be considered when introducing a new species in a plant pathogenic genus.