Abstract Oxalis L. is the largest and most diverse genus in the family Oxalidaceae. Within southern Africa, Oxalis is represented by ca. 270 taxa, the majority occurring in the Cape Region. Although many of the species are widespread, ca. 25% are considered rare. The aim of this paper is to assess the degree of genetic differentiation between two rare and highly localized species ( Oxalis hygrophila Dreyer and Oxalis oligophylla Salter) and the more widespread Oxalis tomentosa L.f. For comparative purposes, we also include Oxalis purpurea L., one of the most widely distributed species in South Africa. Chloroplast sequences of the trnH/ psbA spacer revealed low genetic diversity for O. oligophylla and O. tomentosa compared to the widespread O. purpurea. High genetic diversity in O. purpurea might, in combination with other ecological and reproductive factors, account for the success of this species. In contrast, low variation might contribute to rarity in O. oligophylla and ultimately ground O. tomentosa to become rare. The latter two species were not monophyletic with a shared haplotype. Coalescent modelling revealed low levels of gene flow (< 1 migrant per generation) between them and we argue that the genetic pattern is the result of the retention of ancestral polymorphism following a recent divergence.