Incorporating DNA sequences for ITS, LSU, TEF, ACT and RPB2 from PDD 117678 into the datasets of De Gruyter et al. (Studies in Mycology 75: 1-36, 2012, doi:10.3114/sim0004) and Ariyawansa et al. (Fungal Diversity 74: 19-51, 2015, DOI 10.1007/s13225-015-0349-2), places Rhytidiella hebes in Leptosphaeriaceae, not Cucurbitariaceae. It belongs in a clade with Plenodomus. In this analysis, if Rhytidiella is retained as a genus, this make Plenodomus paraphyletic.

Whether or not the type species of Rhytidiella, R. muriformis is phylogentically the same is not known, but morphologically it is close to R. hebes. The morphology seems to fit reasonably well with Leptosphaeriaceae apart from the large groups of closely-grouped ascomata. Cucurbitariaceae mostly have muriform ascospores.