Phaeodimeriella is an epiphytic or pathogenic genus that occurs on plant surfaces associated with other fungi and belongs in the family Pseudoperisporiaceae (Dothideomycetes family, incertae sedis). The taxonomy of Phaeodimeriella has been problematic because of lack of molecular data and as some of the important morphological characters having not been reported. The present study clarifies the phylogenetic placement of Phaeodimeriella using fresh collections from northern Thailand. Two Phaeodimeriella species are characterized based on combined analyses of LSU, SSU, TEF and RPB2 sequence datasets. In the phylogenetic analyses, the two Phaeodimeriella species form a distinct lineage, adjacent to the Lentitheciaceae and Bambusicolaceae, in the order Pleosporales. The genus Phaeodimeriella is re-described and illustrated using modern concepts from fresh collections and provided with molecular data. The new species Phaeodimeriella cissampeli and P. dilleniae are introduced based on morphological characters, and molecular data is provided. The genus Lizonia is placed in Didymellaceae based on phylogenetic analysis.