This study set out to identify and interpret botanical remains from Historic Cave, Balerno Main Shelter and Balerno Shelter 2 in the Limpopo Province. Botanical remains were identified through comparative collections, and quantified through a raw count and presence analysis. They were interpreted through literature on plant uses in southern Africa. Over 12 500 remains were recovered from Historic Cave, almost 1 500 from Balerno Main Shelter and only five from Balerno Shelter 2. Remains from Historic Cave fell into food, water, storage and muti categories of use. Balerno Main Shelter revealed plants in the water and muti categories. Balerno Shelter 2 had too few remains. The study demonstrated that plant remains can shed light on why cave sites were occupied, as the assemblages reflect different plant uses. The remains from Historic Cave describe a society living and taking refuge in a cave under siege. Balerno Main Shelter may have been used for ritual purposes.