In recent years a serious disease of citrus, Huanglongbing (HLB), associated with ‘Candidatus Liberibacter asiaticus’ (Las), has spread to many new citrus production countries worldwide. South Africa remains free of HLB, but for many years has had a related bacterial species, ‘Ca. Liberibacter africanus’ (Laf), associated with Citrus greening disease (CG). CG is less severe than HLB and is controlled in South Africa through planting healthy certified citrus saplings, removal of infected branches or trees, and control of the triozid vector, Trioza erytreae. Re-infection of new citrus orchards planted in area previous abandoned for citrus production due to CG, suggested the presence of alternate hosts of Laf. This led to the hypothesis that other indigenous Rutaceous trees may be infected with either Laf or Liberibacters related to Laf. One such tree, Calodendrum capense, had been shown in 2000 to host a related bacterial species ‘Ca. Liberibacter africanus spp. capensis’ (LafC). Samples from large numbers of Calodendrum capense, Vepris spp (V. lanceolate or reflexa), Zanthoxylum spp. (Z. capense or Z.davyii), Clausena anisata, Teclea spp. (T. natalensis or gerrardii) and Oricia bachmannii were collected, primarily from within the natural distribution of these trees in South Africa. LafC was found to be widespread in C. capense while unique “Ca. Liberibacter africanus subspecies” were found associated with each tree species with the exception of Oricia, at incidences of between 1 and 11% of sampled specimens. One of these subspecies, “Ca. Liberibacter africanus spp. clausenae (LafCl), was recently observed in citrus. A widely applied Las PCR system, was shown to non-specifically amplify this subspecies in samples from Uganda and Kenya, where Las was recently reported. This casts some doubt on the veracity of this report in these countries.