Species of the genus Trapelia are notoriously variable and difficult to identify. Although previous taxonomic studies have taken advantage of molecular data to confirm the placement and delimitation of species, most Australian taxa, including the recently described T. atrocarpa, T. terrestris and T. rosettiformis, have not been the subject of molecular study. Here, ITS sequences were generated for 11 species of Trapelia occurring in Australia and integrated to a dataset of mostly European Trapelia taxa. As a result, due to poor phylogenetic and morphological differentiations, synonymies are proposed for the three species T. atrocarpa (syn. T. terrestris), T. pruinosa (syn. T. rosettiformis) and T. placodioides (syns T. thieleana and T. occidentalis). Together with a few Welsh T. elacista specimens, T. atrocarpa is found to be closely related to T. elacista. A key to the nine Trapelia species currently accepted from Australia is provided.