In terms of the persistence of biodiversity, the siting of conservation areas has traditionally been ad hoc. In the Cape Floristic Region, a hot-spot of plant biodiversity and endemism, past conservation interventions have led to the mountains being over-represented in the reserve network, while the lowlands have remained very poorly conserved. Ongoing threats to the lowlands such as the rampant spread of invasive alien plants, and land transformation for agriculture and resort development, continue to undermine biodiversity in these regions. A new conservation intervention, the Agulhas National Park, is in the process of being implemented on the coastal lowlands at Africa's southernmost tip. A flexible, reserve-selection design tool is being used to guide this process. The practical challenges in implementing a new protected area in a fragmented landscape, which has a high biodiversity and vulnerability, are examined. The role of different institutions, in partic-in particular state-private partnerships, and current investigations into conservation agencies' policies, legislation and funding mechanisms are dealt with. It is imperative that future conservation planning considers the threats to biodiversity first and foremost. Institutions such as South African National Parks and the Cape Nature Conservation Board must act strategically to avoid changes in land use that will compromise the biodiversity goals of retention and persistence. Conservation efforts will only succeed if institutional and socio-economic considerations are integrated with conservation plans aimed at ensuring the long-term persistence of biodiversity.