Acaena Mutis ex L. (Rosaceae) is the most complex and ecologically variable genus in the subtribe Sanguisorbinae. Although it has been the subject of several taxonomic treatments, the largest phylogenetic analysis to date only sampled a small fraction of the total global diversity (five to seven out of 45 to 50 species). This study included most of the species to elucidate the phylogenetic relationships of Acaena and biogeographic patterns in Sanguisorbinae. Phylogenetic analyses of non-coding nuclear (ITS region) and chloroplast (trnL-F) DNA sequence markers using maximum likelihood and Bayesian analyses suggest that Acaena is a paraphyletic group with species of Margyricarpus and Tetraglochin nested within it. We identified strong support for eight subclades that are geographically or taxonomically structured. Nevertheless, the species-level relationships within subclades are still uncertain, which may be due to rapid diversification and lack of informative characters in the markers used. Sanguisorbinae, a primarily Southern Hemisphere clade, exhibits a classic Gondwana disjunct distribution. This current distribution is explained primarily by long-distance dispersal events (eight in total). Our results suggested that Sanguisorbinae split into Cliffortia and Acaena around 13.6 mya. While Cliffortia diversified in southern South Africa, Acaena experienced several migration events in the Southern Hemisphere. Our estimation of the ancestral range suggested that Acaena likely originated in South Africa, followed by migration into South America and diversification in the temperate regions of Chile and Argentina. From there, the genus migrated to polar and other temperate areas such as New Zealand, throughout the Andes, and to tropical areas in Central America, reaching as far north as California. Our results show that the main sources of propagules for dispersal as well as the greatest diversity for the genus are located in Chile and New Zealand. The evolutionary relationships of species in Acaena combine a history of rapid radiations, long-distance dispersals, and genetic variation within some taxa. Further research should be undertaken to clarify the infraspecific classification of A. magellanica.