The lichenised fungal genus Pyrenula is a very common crustose lichen element in tropical to subtropical forests, but little research has been done on this genus in China. During our study on Pyrenula in China, based on morphological characteristics, chemical traits and molecular phylogenetic analysis (ITS and nuLSU), three new 3-septate species with red or orange oil in over-mature ascospores were found: Pyrenula inspersa sp. nov., P. thailandicoides sp. nov. and P. apiculata sp. nov. Compared to the known 3-septate species of Pyrenula with red or orange oil, P. inspersa is characterised by the inspersed hamathecium; P. thailandicoides is characterised by the IKI+ red hamathecium and the existence of an unknown lichen substance; and P. apiculata is characterised by the absence of endospore layers in the spore tips and the absence of pseudocyphellae. It is reported for the first time that the presence of a gelatinous halo around the ascospores of Pyrenula is common. A word key for the Pyrenula species with red or orange oil in over-mature ascospores is provided. Key words: morphology, new species, phylogeny, Pyrenulaceae, taxonomy.