This study aims to restructure the genus *Diaporthe* by refining its species boundaries using single gene phylogenies (ITS, tef, tub, cal, and his) and multi-gene phylogenies based on GCPSR (Genealogical Concordance Phylogenetic Species Recognition) methodology and coalescence-based models (PTP—Poisson Tree Processes and mPTP—multi-rate Poisson Tree Processes). The genus is divided into seven sections, and the boundaries of 13 species and 15 species-complexes are proposed. The study involved the investigation of 82 *Diaporthe* isolates from woody hosts in Guizhou Province, China, leading to the discovery of two novel species and the recognition of 17 previously known species. Synonymies are specified for 31 species based on molecular data and morphological studies. The re-structuring of the genus into sections based on phylogenetic analyses avoids the construction of lengthy phylogenetic trees and simplifies future taxonomic studies. The results provide a clear framework for taxonomists, mycologists, and plant pathologists to address the challenges in species identification and management.This study aims to restructure the genus *Diaporthe* by refining its species boundaries using single gene phylogenies (ITS, tef, tub, cal, and his) and multi-gene phylogenies based on GCPSR (Genealogical Concordance Phylogenetic Species Recognition) methodology and coalescence-based models (PTP—Poisson Tree Processes and mPTP—multi-rate Poisson Tree Processes). The genus is divided into seven sections, and the boundaries of 13 species and 15 species-complexes are proposed. The study involved the investigation of 82 *Diaporthe* isolates from woody hosts in Guizhou Province, China, leading to the discovery of two novel species and the recognition of 17 previously known species. Synonymies are specified for 31 species based on molecular data and morphological studies. The re-structuring of the genus into sections based on phylogenetic analyses avoids the construction of lengthy phylogenetic trees and simplifies future taxonomic studies. The results provide a clear framework for taxonomists, mycologists, and plant pathologists to address the challenges in species identification and management.