To better understand biogeographic patterns in the Southern Hemisphere, infraspecific molecular patterns were compared in two species of the moss genus Calyptrochaeta with contrasting distributions. One, C. apiculata, has a disjunct distribution encompassing South America and Australasia, and the other, C. asplenioides, occurs from South Africa northward to Rwanda and eastward into the Indian Ocean Islands. Nucleotide sequence data from two plastid loci (trnL-F and trnG) and nuclear ribosomal DNA (ITS1–2) were gathered from 62 samples representing the genera Calyptrochaeta and Daltonia (the latter as an outgroup), and subjected to phylogenetic analyses using maximum likelihood and Bayesian inference. The phylogenetic analyses revealed strong, geographically correlated structure within C. asplenioides in which populations from southern Africa are sister to those from eastern Africa, Madagascar, and the other Indian Ocean islands. Continental plants are further differentiated from island plants to the east. Divergence times suggest that C. asplenioides diversified in a time frame that does not support vicariance associated with continental drift, but rather dispersal, to explain the disjunct distribution of this species. Sequences of C. apiculata disjunct between Chile and Australia are nearly identical, which strongly suggests recent and/or ongoing gene flow. Our dating suggests that the South American-Australian disjunction of C. apiculata is also not old enough to reflect vicariance associated with continental drift. Thus, in both cases, recent long distance dispersal best explains their distributions in the Southern Hemisphere.