A group of eight species of Encephalartos, comprising E. altensteinii, E. arenarius, E. horridus, E. latifrons, E. lehmannii, E. longifolius, E. princeps, and E. trispinosus, from the Eastern Cape Province of South Africa, was studied by analysis of iso-enzymes, ribosome DNA, and ITS 1 and 2 genes. The reason for this investigation was that the morphology of the vegetative and reproductive parts, though very distinctive in this geographical region, do not correlate, and it was hoped that molecular data would elucidate evolutionary relationships. The three sets of molecular data were found to agree to a remarkable degree. It was concluded that the vegetative morphology was misleading but that the cone characteristics agree with molecular data and provide insight into the interrelationships of these species. Thus, E. princeps was concluded to be relatively remotely related to the vegetatively similar E. lehmannii, and E. arenarius is not at all close to E. latifrons even though the two species are easy to confuse when not in cone.