Resolving the relationships between genera in the lichen family Tephromelataceae has proven difficult and the taxon limits within the genus Calvitimela are only partly understood. In this study, we test the monophyly of Calvitimela and provide recommendations for an updated classification of the genus through an integrative taxonomic approach. Freshly collected material from Norway and fungarium specimens of all species currently assigned to Calvitimela (including available holotype and isotype material) formed the foundations for the study. Additional population sampling of Calvitimela melaleuca s. lat. was performed to investigate the relationship between secondary metabolite chemistry and genetic lineages recovered by the ITS marker. Chemical and morphological characters were analyzed to test their diagnostic values in the genus. More than 300 sequences from five different loci (ITS, LSU, MCM7, mtSSU, TEF1-?) were produced and used, together with existing molecular data, to infer phylogenetic relationships in Calvitimela. Our molecular phylogenetic results show that the C. armeniaca-melaleuca species complex constitutes four distinct genetic lineages. Moreover, detailed morphological examinations of C. melaleuca s. lat. reveal differences between taxa previously assumed to be morphologically cryptic. Secondary metabolite chemistries are found to be overlapping between divergent genetic lineages across the genus. Population level analyses of C. melaleuca s. lat. corroborates both phylogenetic and chemical results. Phylogenetic analysis of the mtSSU suggests that the Antarctic species C. uniseptata belongs in Thamnolecania (Ramalinaceae). One new grouping in the C. aglaea complex, phenotypically close to C. perlata, is recognized and proposed as a new species. We also find molecular evidence for C. septentrionalis being sister to C. cuprea. We discuss the role of cryptic diversity in an evolutionary context and explore the potential reasons for non-monophyly in Calvitimela and poor intergeneric resolution in the family Tephromelataceae.