The aim of this research was to identify the wealth of secondary metabolites in the Chilean lichen Sticta caulescens, applying green chemistry approaches and comparing the following two extraction methods: (a) conventional maceration with methanol, and (b) microwave-assisted extraction (MAE) using ethyl lactate as a solvent. In addition, chemoinformatic and chemotaxonomic studies were conducted on S. caulescens and other species of the genus Sticta, which have been reported in previous studies. A UHPLC/ESI-MS/MS analysis allowed for the identification of 32 metabolites obtained from maceration and 33 from MAE, considering carbohydrates, aromatic compounds, acids, depsides, depsidones, dibenzofurans, lipids, anthraquinones, and triterpenes. Maceration using methanol yielded a slightly higher extract percentage than with ethyl lactate (6.3% versus 5.0%), while MAE extracted an almost identical spectrum of metabolites using ethyl lactate,—though including one compound detected only under MAE conditions. This highlighted both the method efficiency and selectivity. This study also incorporates a comprehensive chemoinformatic and chemotaxonomic analysis of secondary metabolites across 12 Sticta species. A computational comparison (Morgan fingerprints, Jaccard similarity, hierarchical clustering, Murcko scaffolds) demonstrated that S. caulescens is one of the most chemically diverse species, closely related to S. cordillerana, and forming part of a major chemotaxonomic lineage, which is characterized by high scaffold richness and shared aromatic/depsidone biosynthetic pathways. Keywords: Sticta caulescens; ethyl lactate; Green extraction; microwave; non-conventional technology; chemotaxonomic analysis.