Despite their importance in bio-deterioration, the taxonomy of the calcicolous endolithic lichen genus Bagliettoa is still problematic, mostly because of difficult identifications and unsettled species concepts. In this study, the traditional morphology-based species and genus delimitations were tested using the phylogenetic markers ITS, mcm7 and mtSSU. Bayesian and maximum likelihood approaches were used on a dataset of 82 specimens to reconstruct phylogenetic relationships between the eight most common species ofBagliettoa. Molecular data confirmed the placement ofB. limborioides, the type of the generic name, within the clade including species usually considered as part of Bagliettoa. Five other species were monophyletic and well supported (B. baldensis, B. calciseda, B. cazzae, B. marmorea, B. parmigerella). Relationships within a clade including B. parmigera, B. steineri and specimens with intermediate characters (here referred to as B. cf suzaeana) were not resolved and weakly supported. This species complex (also called B. parmigera s.1.) is in need of a further revision. After revision of the type material, a lectotype is chosen for Bagliettoa parmigerella. Additionally, the new combinations Bagliettoa rubrocincta and Bagliettoa suzaeana are proposed based on their morphological similarity to other species of Bagliettoa. A key to the 12 currently recognized species is provided, which will hopefully help ecologists and biogeologists to identify species from this difficult genus of endolithic lichens.