The generic placement of the strawberry leaf blight fungus, formerly known as Phomopsis obscurans has always been subject to uncertainty. These datasets provide the phylogenetic evidence based on four DNA markers (28S rDNA/LSU, ITS, TEF1 and RPB2) that support the establishment of a monotypic new fungal genus Paraphomopsis. Datasets include the single gene sequence alignments for the LSU, ITS, TEF1 and RPB2 markers, and the complete combined phylogenetic dataset and phylogenetic tree files for each single gene and combined analysis. The updated multi-gene datasets and trees for the Diaporthales provide the evidence to distinguish the leaf blight pathogen (Paraphomopsis obscurans) from the taxa associated with leaf blotch (Gnomoniopsis fragariae) and petiole blight and root rot (Paragnomonia fragariae). Resources in this dataset:Resource Title: Combined LSU_ITS_RPB_TEF1 DNA sequence alignment_Diaporthales. File Name: 1_Combined_LSU_ITS_RPB_TEF1_DNA sequence alignment_Diaporthales.txtResource Title: Combined LSU_ITS_RPB_TEF1 ML tree Diaporthales. File Name: 2_Combined tree_LSU_ITS_RPB_TEF1_ML tree_Diaporthales.txtResource Title: ITS_DNA sequence alignment Diaporthales. File Name: 3_ITS_DNA sequence alignment_Diaporthales.txtResource Title: ITS single gene ML tree Diaporthales. File Name: 4_ITS_single gene ML tree_Diaporthales.txtResource Title: LSU_DNA sequence alignment Diaporthales. File Name: 5_LSU_DNA sequence alignment_Diaporthales.txtResource Title: LSU_single gene ML tree Diaporthales. File Name: 6_LSU_single gene ML tree_Diaporthales.txtResource Title: RPB2_DNA sequence alignment Diaporthales. File Name: 7_RPB2_DNA sequence alignment_Diaporthales.txtResource Title: RPB2_single gene ML tree Diaporthales. File Name: 8_RPB2_single gene ML tree_Diaporthales.txtResource Title: TEF1_DNA sequence alignment Diaporthales. File Name: 9_TEF1_DNA sequence alignment_Diaporthales.txtResource Title: TEF1_single gene ML tree Diaporthales. File Name: 10_TEF1_single gene ML tree_Diaporthales.txt