We utilized ITS and mtSSU sequence data to study the phylogenetic relationships of Lepraria samples collected in the Southern Hemisphere, including Australia, Chile, New Zealand and Antarctica. Morphological characters and the secondary chemistry of the specimens were also examined. Using a combination of morphological, chemical and molecular data, we identified nine lineages in our material. The lineages are: Lepraria toilenae, L. eburnea, L. nothofagi, L. straminea, L. caerulescens, L. finkii, and three previously undescribed clades that are here described as L. chileana, L. neozelandica and L. ulrikii. The first is described from Chile. The second occurs in New Zealand, and the third has an Australasian distribution, occurring in New Zealand, mainland Australia, and Tasmania. In addition, L. straminea is identified as an usnic acid-producing species of the genus Lepraria. Moreover, L. caerulescens is confirmed as a distinct species.