Species delimitations in the predominantly Antarctic and South American group of neuropogonoid species of the lichen-forming fungal genus Usnea are poorly understood. Morphological variability has been interpreted as a result of harsh ecological conditions, but preliminary molecular data have led to doubts about the current species delimitations in these lichenized fungi. We examined species boundaries using a phylogenetic approach and a cohesion species recognition method generating haplotype networks and looking at associations of phenotypic characters with clades found in the networks. In addition, we estimated gene flow among detected clades and currently circumscribed species. We identified several clades that were significantly associated with phenotypic characters, but did not necessarily agree with current species circumscriptions. In one case (U. aurantiaco-atra/U. antarctica), network analysis and the estimation of gene flow provided no evidence of distinct species. The distinctness of another species pair (U. subantarctica/U. trachycarpa) remains dubious, showing evidence for gene flow among currently accepted species.