The origin of two tetraploid species of Hordeum, H. capense from South Africa and H. secalinum from Eurasia and North Africa, is explored using phylogenetic analyses of two single-copy nuclear genes (DMC1 and EF-G) and one plastid gene (rbcL). By applying copy-specific primers it was possible to obtain sequence data from two copies of each of the nuclear genes from the two tetraploid species. The most parsimonious explanation of the presence of both genes is that each copy was inherited from a different diploid parental species. Hence, H. capense and H. secalinum are allotetraploids. The phylogenetic analyses also demonstrated that the two species have a common hybrid origin involving diploid H. marinum subsp. gussoneanum and H. brevisubulatum. A gene tree derived from the plastid rbcL sequences showed that H. brevisubulatum was the maternal parent. Based on the number of evolutionary changes since polyploidization and subsequent diversification of the two species, H. capense, with an isolated occurrence in South Africa, is best explained as an ancient relict, as opposed to a recent introduction.