This study re-evaluates the genus Diaporthe, aiming to refine species and species-complex boundaries. Diaporthe is a significant plant pathogen, occurring as endophytes and saprobic fungi. Many morphologically similar species are genetically distinct, leading to overestimation or underestimation of species numbers. The study uses single and multi-gene phylogenies, along with coalescence-based models (PTP and mPTP), to restructure the genus into seven sections. It proposes boundaries for 13 species and 15 species-complexes. Analysis of 82 isolates from Guizhou Province revealed two novel species and 17 known ones. Synonymies for 31 species are provided. The study suggests dividing Diaporthe into sections to avoid lengthy phylogenetic trees in future research. Species from the appropriate section should be selected for phylogenetic analysis. The genus is divided into seven sections: Betulicola, Crotalariae, Eres, Foeniculina, Psoraleae-pinnatae, Rudis, and Sojae. Each section contains several species and species-complexes. The study proposes 28 species-species-complexes, with names based on the oldest epithet or species popularity. The results are deposited in TreeBASE and the Faces of Fungi database. The study highlights the importance of molecular data in species identification and taxonomy. The findings provide a baseline for taxonomists, mycologists, and plant pathologists dealing with Diaporthe. The study also emphasizes the need for integrating molecular data with morphology for accurate species delimitation. The results suggest that some species-complexes should be considered single species rather than multiple. The study provides detailed descriptions and synonyms for several Diaporthe species, including Diaporthe anacardii, Diaporthe arecae, Diaporthe biconispora, Diaporthe foeniculina, and others. The study concludes that the genus Diaporthe should be restructured into seven sections, with clear boundaries for species and species-complexes. The findings contribute to a better understanding of Diaporthe taxonomy and species boundaries.This study re-evaluates the genus Diaporthe, aiming to refine species and species-complex boundaries. Diaporthe is a significant plant pathogen, occurring as endophytes and saprobic fungi. Many morphologically similar species are genetically distinct, leading to overestimation or underestimation of species numbers. The study uses single and multi-gene phylogenies, along with coalescence-based models (PTP and mPTP), to restructure the genus into seven sections. It proposes boundaries for 13 species and 15 species-complexes. Analysis of 82 isolates from Guizhou Province revealed two novel species and 17 known ones. Synonymies for 31 species are provided. The study suggests dividing Diaporthe into sections to avoid lengthy phylogenetic trees in future research. Species from the appropriate section should be selected for phylogenetic analysis. The genus is divided into seven sections: Betulicola, Crotalariae, Eres, Foeniculina, Psoraleae-pinnatae, Rudis, and Sojae. Each section contains several species and species-complexes. The study proposes 28 species-species-complexes, with names based on the oldest epithet or species popularity. The results are deposited in TreeBASE and the Faces of Fungi database. The study highlights the importance of molecular data in species identification and taxonomy. The findings provide a baseline for taxonomists, mycologists, and plant pathologists dealing with Diaporthe. The study also emphasizes the need for integrating molecular data with morphology for accurate species delimitation. The results suggest that some species-complexes should be considered single species rather than multiple. The study provides detailed descriptions and synonyms for several Diaporthe species, including Diaporthe anacardii, Diaporthe arecae, Diaporthe biconispora, Diaporthe foeniculina, and others. The study concludes that the genus Diaporthe should be restructured into seven sections, with clear boundaries for species and species-complexes. The findings contribute to a better understanding of Diaporthe taxonomy and species boundaries.