Meristematic fungi are mainly defined as having aggregates of thick-walled, melanised cells enlarging and reproducing by isodiametric division. Dothideomycetes black meristematic and meristematic-like fungi have been allied to Myriangiales, which currently has two accepted families, Myriangiaceae and Elsinoaceae, with fungi mainly regarded as pathogens, parasites, saprobes and epiphytes of different plant species. This study aimed to verify the phylogenetic position using four nuclear markers (SSU, LSU, ITS and RPB2) of the incertae sedis genera associated with Myriangiales, namely Endosporium, Gobabebomyces, Lembosiniella and Phaeosclera, and the new genus, Endophytium gen. nov. (including E. albocacti sp. nov. and E. cacti sp. nov.), established for endophytic fungi occurring in cacti in Brazil. Based on morphology, lifestyle and phylogenetic inferences, these black meristematic and meristematic-like fungi cannot be accommodated in Myriangiales. Combining these results, three new orders and two new families are introduced: Endophytiales ord. nov. (including Endophytiaceae fam. nov. for Endophytium gen. nov.), Endosporiales ord. nov. (including Endosporiaceae for Endosporium) and Phaeosclerales ord. nov. (including Phaeoscleraceae fam. nov. for Phaeosclera). Gobabebomyces and Lembosiniella remained incertae sedis due to their disposition in the phylogenetic tree, that moved among clades accordingly with the gene analysed. Our results show that the inclusion of endophytic fungi obtained from plants in dry forests can contribute to the discovery of new taxa, clarify the phylogenetic position of allied taxa and confer information to the estimation of national and global fungal diversity.