The transoceanic disjunct distributions between Australasia and Austral America have been observed in many plant groups. The processes behind these disjunct distributions remain a source of debate due to differences in species vagility, biogeographical history, and complex geological and climatic changes. We address the phylogenetic relationships and biogeographical history of the austral hornwort genus Phaeomegaceros based on eight molecular markers from the three genomes (nuclear: phytochrome, mitochondrial: nad5, and chloroplast: rbcL, trnL intron, trnL-trnF spacer, rps4 gene, rps4-trnS spacer, and matK gene). With ten taxa based on morphological and molecular data, the three phylogenetic analyses supported the genus Phaeomegaceros as monophyletic. Phaeomegaceros is composed of two major clades corresponding to the New Zealand species, which presents a conspicuous trilete mark with one depression in the middle of the spore’s proximal face, and the Austral American species, which lack this middle depression. Dating and biogeographical analyses indicate that the Phaeomegaceros ancestral area was New Zealand and Antarctica in the Late Cretaceous (53.51 Ma, HPD 95% = 31.64–72.63). While Austral American species diverged during the Eocene. We speculate that climatic fluctuations in the Antarctic continent during the middle to late-Miocene led to the isolation of Phaeomegaceros taxa with both processes (dispersal events and vicariance) acting on the independent evolution of the disjunct clades. Furthermore, recent diversification of Phaeomegaceros taxa in Austral America and range expansion to northern Andes and oceanic islands, are explained by dispersal events and subsequent cladogenesis coinciding with the uplift of the Andes and the formation of volcanic oceanic islands (Juan Fernandez and Tristan da Cunha).