Projected climate change has been suspected of affecting the biota of conserved nature areas in different and significant ways. Nevertheless, strategic management within some nature conservation agencies appears relatively unprepared for the possible consequences of climate change. National level planning of reserve design networks has also tended to skirt the issue, possibly owing to insufficient analysis. This paper provides a first assessment of the possible effects of climate change on plant diversity within the protected area network of South Africa. A climate change scenario of increased temperature but no change in precipitation resulted in derived optimum growth days increasing in some reserves through increased temperature extending the growing season. In some other reserves optimum growth days declined through greater evapotranspiration. We concentrated on the larger reserves of the latter group for which conditions that are more limiting were predicted. Plant species were evaluated in terms of their critical limits in growth days and minimum temperature. Over a third of the species analysed for one reserve (Augrabies Falls National Park and Melkbosrand) was indicated to become locally extinct with climate change. Another reserve in the region showed fewer than 1% local extinctions. It is clear that although a certain magnitude of climate change is a prerequisite for these extinctions, the rate and number of extinctions depend strongly on the different environmental tolerances of the specific biotic components of the conserved area. Potential immigration of other species to Augrabies Falls/Melkbosrand required to balance the projected extinctions with climate change would need migration abilities and conditions that are unlikely to be met. A net decrease in plant diversity may thus be expected. The results confirm that with the climate change scenario used, the concept of sustaining species through fixed protected areas may be fundamentally flawed, at least in certain areas.