Little urban ecological research has been done in South Africa. The papers in the Ecology and Society special feature Urban Ecological and Social-Ecological Research in the City of Cape Town make, therefore, an important contribution to the development of urban ecology locally and globally. Different approaches have been used in the study of urban ecology of different urban areas in South Africa. Cape Town is situated in a biodiversity hotspot and is the only South African city which includes a national park. As a result the urban ecological studies were mainly driven by urban nature conservation concerns. In other cities such as Durban, open space planning and environmental management were the major issues which focused ecological studies on urban areas whereas other studies of urban areas in the Eastern Cape and North-West provinces included private and public open spaces and man-made habitats. We reflect on the Cape Town studies in a South African context and highlight conservation of biodiversity, protection of ecosystem services, management of control measures, and the conflict between humans and nature. A brief synthesis has also been given of South African urban ecological research in general.