Species delimitation among closely related species is challenging because traditional phenotype-based approaches, e.g., morphology, ecological, or chemical characteristics, often produce conflicting results. With the advent of high-throughput sequencing, it has become increasingly cost-effective to acquire genome-scale data which can resolve previously ambiguous species boundaries. As the availability of genome-scale data has increased, numerous species delimitation analyses, such as BPP and SNAPP+Bayes factor delimitation (BFD*), have been developed to delimit species boundaries. However, even empirical molecular species delimitation approaches can be biased by confounding evolutionary factors, e.g., hybridization/introgression and incomplete lineage sorting, and computational limitations. Here we investigate species boundaries and the potential for micro-endemism in a lineage of lichen-forming fungi, Niebla Rundel & Bowler in the family Ramalinaceae. The species delimitation models tend to support more specious groupings, but were unable to infer robust, consistent species delimitations. The results of our study highlight the problem of delimiting species, particularly in groups such as Niebla, with complex, recent phylogeographic histories.