Peltigera (Peltigerineae, lichenized Ascomycota) is one of the most widespread lichen genera incorporating bi‐ and trimembered associations involving fungi, green algae (cf. Coccomyxa), and cyanobacteria (cf. Nostoc). A wide range of morphological and chemical (secondary compounds) variation at both the intra‐ and interspecific levels is present in this genus. Compared to many other genera of macrolichens, its taxonomy, including chemotaxonomy, still remains poorly understood. Existing infrageneric classifications of Peltigera are almost exclusively based on photobiont composition of the thallus. These classifications assumed that bi‐ and trimembered taxa were distinct monophyletic entities. The genus Peltigera has never been the focus of a comprehensive phylogenetic study. The most recent and widely accepted subdivision of the genus into seven groups is based mainly on morphological and chemical characters. Relationships among species of Peltigera are investigated here using chemical, morphological, and large subunit nuclear ribosomal DNA (LSU nrDNA) data. We test the monophyly of these seven morpho‐chemical Peltigera groups and propose a classification based on a phylogenetic approach. Data sets of 42 chemical characters (terpenoids), 31 morphological characters, and 1135 LSU nrDNA characters for 96 samples representing 38 Peltigera species, eight undescribed putative Peltigera species, and nine species from seven potentially closely related genera from Peltigerineae were subjected to maximum parsimony analyses. Morphological, chemical, and molecular analyses were carried out independently and on a combined data set. Monophyly of Peltigera, including Hydrothyria, was confirmed. The genus Hydrothyria is transferred to Peltigera and a new combination Peltigera hydrothyria Miadlikowska & Lutzoni is proposed. Eight monophyletic sections within the genus Peltigera, with high bootstrap support, are circumscribed: sections Peltigera, Polydactylon Miadlikowska & Lutzoni, Chloropeltigera Gyeln., Peltidea (Ach.) Vain., Horizontales Miadlikowska & Lutzoni, Retifoveatae Miadlikowska & Lutzoni, Phlebia Wallr., and Hydrothyriae Miadlikowska & Lutzoni. Unequivocal morphological and chemical synapomorphies for all sections except section Peltidea are recognized and presented. A key for identification of the sections is provided. In addition, a key based on four main terpenoids for determination of the chemotypes and species within section Polydactylon is included. Five terpenoids (50–54) identified on thin‐layer chromatography plates for P. elisabethae and P. horizontalis chemotype I are added to the list of substances found in Peltigera. Five chemotypes, mainly from Poland and Norway, are reported from Peltigera thalli for the first time: P. malacea chemotype V, P. leucophlebia chemotype II, P. hymenina chemotypes II and III, and P. collina chemotype IV. Three main types of vein structure in Peltigera were recognized based on SEM studies.