The aim of this work was to study a fast, new, sensitive, and simple method for the chemotaxonomic classification of Chilean lichens (Teloschistes chrysophthalmus, Ramalina farinacea, Usnea pusilla, Ramalina chilensis and Stereocaulon ramulosum) using MALDI-TOF-MS and UPLC-ESI(-)-MS data. Lichens soluble proteins fingerprints were acquired by MALDI-TOF-MS and they were analyzed by chemometric (PCA). Lichens organic extracts fingerprints were obtained by UPLC-ESI(-)-MS. MALDI-TOF-MS associated with chemometric analysis was used to detect new m/z patterns of soluble proteins that were compared with Protein Data Bank of UnitPro. These data also permitted the satisfactory distinction among the families and species. UPLC-ESI(-)-MS fingerprints analyses of the organic extracts showed the presence of five major lichen compounds (atranorin, parietin, teloschistin, ramalinolic and usnic acids). In contrast to other techniques, MALDI-TOF-MS associated with chemometric analysis and UPLC-ESI(-)-MS provided a new, fast and sensitive method for chemotaxonomic characterization of lichens.