Pyrenula sanguinea Aptroot, M. Cáceres & Lücking is described from branches of trees in Amazonian rain forest in the state of Rondônia, Brazil. It is characterized by bright red, pseudostromatic ascomata with fused walls, closely resembling those of Trypethelium eluteriae and related species except for the color. The brown ascospores deviate from those of most other Pyrenula species by their reduced endospore formation; they are surrounded by a thick gelatinous sheath with horn-like and curled appendages at the tips. Although morphologically very distinct from all other known species of Pyrenula, molecular data of the mtSSU and nuLSU loci revealed that it is nested within that genus, with a strongly supported sister-group relationship with P. cruenta. Both species share the bright red color of ascomata, but co-chromatography revealed a distinct, complex pattern for P. sanguinea, with six different pigments, only haematommone shared with P. cruenta.