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The lichen-forming fungal genus Flavoparmeliaincludes species with distinct distribution patterns, including subcosmopolitan, restricted, and disjunct species. We used a dataset of nuclear ITS and LSU ribosomal DNA including 51 specimens to understand the influence of historical events on the current distribution patterns in the genus. We employed Bayesian, maximum likelihood and maximum parsimony approaches for phylogenetic analyses, a likelihood-based approach to ancestral area reconstruction, and a Bayesian approach to estimate divergence times of major lineages within the genus. We identified two major clades in the genus, one of them separating into two subclades and one of those into four groups. Several of the groups and clades have restricted geographical ranges in the Southern Hemisphere, but two groups include species with wider distribution areas. Our analyses suggest that the genus originated in southern South America during the Eocene–Oligocene transition and that the diversification of the Australasian groups occurred recently. The subcosmopolitan distribution of species is explained by long-distance dispersal, while vicariance probably played a major role in the origin of the genus. Several currently accepted species were found to be non-monophyletic, indicating that the species delimitation in the genus requires further studies.