M.Sc. (Botany) / Rhynchosia is a genus within the tribe Phaseoleae, a group of papilionoid legumes that are economically important both for human and animal consumption because of their high protein content. The genus is pantropically distributed and comprises ca. 230 species. South African species were last studied by Baker in 1923. He identified five sections based on their morphological structures. No molecular studies have been carried out on the species to support the taxonomic classification. A systematic study of the relationship within the species was undertaken using five markers; matK, rbcL, trnH-psbA, rpl32-trnL and Internal Transcribed Spacer (ITS) as well as morphological characters, to investigate phylogenetic relationships in the genus Rhynchosia. Results obtained from a combined analysis produced four clades, two of which (clade three and four) received strong support from Bayesian Inference analyses, two of which received low BI support and therefore referred to as groups. Sections Chrysoscias, Polytropia, Arcyphyllum and Cyanospermum are embedded within a paraphyletic type section Rhynchosia. The results further suggest that sections Polytropia and Chrysoscias, which possess a high density of glands on the leaves, are very closely related forming a clade with species from section Rhynchosia. The morphologically distinct species R. monophylla came out as sister to all four clades.