Contributing to the process of reassigning lecideoid lichens to natural taxa, we assessed phylogenetic relationships and species delimitation in the Calvitimela aglaea complex (Tephromelataceae) using DNA sequence data and morphological/anatomical and chemical characters. Phylogenetic analysis of nuclear (ITS, MCM7, TEF1-α) and mitochondrial (ribosomal SSU) DNA sequences revealed Mycoblastus as sister to a strongly supported clade comprising Calvitimela, Tephrolema and Violella. Species of these three genera fall into six strongly supported subclades with low backbone resolution. Two of these are represented by Tephromela and Violella, which are readily circumscribed morphologically. The remaining four subclades encompass lineages that have until now been assigned to Calvitimela. While Tephromela and Violella as currently circumscribed are recovered as monophyletic in our analyses, Calvitimela is paraphyletic, with four deeply divergent clades. We recognize these four clades as subgenera Calomela, Calvitimela, Paramela and Severidea. Our molecular results further support the recognition of two recently discovered sterile crusts as new species, Calvitimela cuprea and C. livida, distinguished from previously known species by their production of asexual diaspores and from each other by secondary metabolite chemistry. We also report Calvitimela perlata as new for continental North America.