We describe the new species Alloarthopyrenia aptrootiana from western Mexico, representing the second known species in the genus and its first tropical member. The new species is characterized by its narrow, 1-septate ascospores of 17–21 × 6–7.5 μm, with additional strong constrictions in the middle of each cell. We present a phylogeny of Trypetheliaceae that confirms the position of the new species in the genus. We propose the new combination Naetrocymbe cinereopruinosa to accommodate the historically misapplied Arthopyrenia cinereopruinosa based on its type collection and confirm Alloarthopyrenia italica as a different and valid species. Based on our phylogenetic analysis, we also propose the new combination Pseudobogoriella confusa to accommodate a species previously known in the genus Mycomicrothelia. Key words: Arthopyrenia, Chamela-Cuixmala Biosphere Reserve, lichens, Mexico, Naetrocymbe cinereopruinosa, phylogeny, Pseudobogoriella confusa, tropical dry forest.