In this study we present an analysis of the Pyrenula ochraceoflava group (Pyrenulaceae), focusing on the Neotropics and based on morphological, chemical, and molecular data of the mtSSU, nuLSU and ITS markers. We described three new species from tropical dry forests of Mexico, confirm the monophyly of the P. ochraceoflava group and provide evidence for the inclusion of species currently placed in the genus Mazaediothecium within Pyrenula. Pyrenula aurantiacoretis sp. nov. is characterized by an orange pigment covering the thallus in net-like fashion, muriform ascospores with 4 rows of 1–4 cells each, 12–15.5 x 8– 10.5 µm, and 7-chloroemodin and emodin as major compounds. Pyrenula connexa sp. nov. is closely related to Mazaediothecium album, being characterized by mazaedioid pyrenocarps, basal and lateral excipular carbonization, highly variable mature ascospores, 1-septate to submuriform, thallus with abundant white verrucae, and lichexanthone as major compound. Pyrenula moldenkeorum sp. nov. is characterized by an orange thallus, submuriform ascospores that frequently show pigmented septa forming a cross septation pattern, 7.5–11 x 5.5–8.5 µm in size, and 7-chloroemodin and emodin as major compounds. The taxonomy of the most common and widespread species of the group, P. ochraceoflava and P. ochraceoflavens, is briefly discussed, presenting evidence to support the consideration of P. ochraceoflava as a species complex. The two species Mazaedothecium album and M. mohamedii are transferred to Pyrenula as P. aptrootiana nom. nov. [non Pyrenula alba (Schrad.) A.Massal.] and P. mohamedii comb. nov. Keywords: Lichen systematics, biodiversity, Neotropics, Mexico, Cuba, Brazil, Chamela Biological Station, Pyrenula aurantiacoretis, Pyrenula connexa, Pyrenula moldenkeorum.