Abstract The current taxonomy of Pelargonium reniforme recognises two subspecies on the basis of habit and vegetative characters, but excludes floral characters. However, populations of P. reniforme in the wild tend to belong to easily discernable floral groups based on floral colour and hypanthium length. The aim of this study was to determine the genetic diversity within and between populations of both subspecies using the Inter-Simple Sequence Repeat (ISSR) method of DNA fingerprinting. Ninety individuals from eight populations were sampled. Both phenetic and Neighbor-Net analyses reveal that populations are genetically discernable, but that there is no genetic evidence to support the recognition of the two currently defined subspecies of P. reniforme. Instead, the analyses resolved all individuals that possess long hypanthia into a single group, and the role of different pollinators in driving reproductive isolation of this long-tubed form is suggested.