Species boundaries in lichen-forming fungi occurring in extra-tropical regions are relatively well studied in comparison with those in species distributed in tropical regions. Here, we aim to re-examine species boundaries in two pantropical, asexually reproducing species, Bulbothrix isidiza and B. tabacina. We generated a multi-locus DNA sequence data set from samples collected throughout the Tropics and these data were analysed in a phylogenetic framework. Our results show that B. isidiza and B. tabacina, as currently circumscribed, do not form monophyletic groups. Rather, our study supports the presence of five, independent species-level lineages in B. isidiza s.l. and three in B. tabacina s.l. Additionally, seven other species were recovered in distinct lineages. Some of the previously overlooked lineages appear to have a restricted geography, whereas others are pantropical. Morphological, chemical and ecological features were re-evaluated for each of these lineages. A new species, B. kenyana sp. nov., is formally described from East Africa and a new combination, B. sublaevigatoides comb. nov., is proposed. Due to limited specimen sampling, the remaining undescribed species-level lineages newly circumscribed in this study are not formally recognized here.