Lumbsch & Huhndorf (2010) and Hyde et al. (2013) placed Endococcus in Dothideomycetes genera incertae sedis. In the present study we refer it to the family Lichenotheliaceae based on morphological similarity with the type species of Lichenothelia (Lichenothelia scopularia (Nyl.) D. Hawksw.), which colonizes diverse types of rock substrates and is sometimes found on lichens. Due to the perithecioid ascomata with widely porate ostioles, globose to broadly clavate asci and hyaline or brown, 1-septate ascospores, we regard Endococcus as a distinct genus in the family Lichenotheliaceae. Index Fugorum lists79 species in this genus but none have had their placement confirmed by molecular data. From studies of morphology they have been put into different families, hence this group is obviously polyphyletic. In this study we only re-examined the type species, Endococcus rugulosus.