This study examined the phylogenetic status of Phlyctis atomella, known from the Western Ghats, based on an integrative taxonomic approach which included morphology, anatomy, chemistry, and molecular phylogeny. Despite the existence of 26 documented species in Phlyctis worldwide, molecular sequence data is presently accessible solely for five of these species. Analysis based on concate-nated ITS and mtSSU data suggests the placement of P. atomella within Phlyctis either as an early diverging lineage or a delineated poorly supported sister to P. boliviensis. This is the first molecular phylogenetic study of the crustose lichen genus Phlyctis based on fresh collections from India.