Despite their importance in ecosystems and biodiversity, very little is known about the health of trees in the native environments of South Africa. The vision and primary goal of the Centre of Excellence in Tree Health Biotechnology (CTHB) is therefore to promote the health of native trees by making use of biotechnology. In this paper, we use the CTHB as an example to explore the positive impacts of the Department of Science and Technology's Centre of Excellence programme on the science system of South Africa and, furthermore, to consider the programme's overall contribution to the strategic priorities set out in the South African Government's Medium Term Strategic Framework that guides the national mandate. We also discuss briefly how the outputs of the CTHB are put into practice in the form of tangible services provided to stakeholders from all sectors ranging from academia, the forestry industry and the general public through to government. Finally, we consider the various factors that have contributed to the success of the CTHB and conclude with a reflection on the far-reaching effects that a relatively small investment by the Department of Science and Technology has had on research and development in South Africa. This is not only in terms of human capacity development, but also overall research excellence. For the CTHB specifically, this initiative also has facilitated a deep appreciation of the factors threatening the health of native trees. Such knowledge provides a crucial foundation towards our understanding of the challenges associated with trees in native woody ecosystems and those propagated commercially, which have emerged and will continue to emerge as a result of trade, transport and tourism, as well as climate change.