We have investigated the size class distribution (SCD) of baobabs on a rocky outcrop, known alternatively as Kubu or Lekhubu, located in the southwest of Sowa Pan, northern Botswana. This study is aimed primarily at determining whether baobab girths show any systematic distribution relative to elevation, linked to palaeo-lake levels during the late Holocene. A secondary objective was to determine whether the SCD of the species might reflect late Holocene climatic changes. Our data show no systematic link between baobab size and elevation, and that the distribution of the species on the outcrop does not provide evidence for former levels of the palaeo-lake. Rather, the population structure is strongly influenced by large, old baobabs, which have provided localized long-lived seed centres favourable for sporadic germination and recruitment to the Kubu population. The broadly unimodal SCD of the Kubu baobab population does not appear to reflect climate changes over the lifespan of the species (up to ~1500 years). This is most likely linked to the development pattern of the species, with rapid growth over the first quarter to half of the tree's life, followed by subsequent very slow growth rates.