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This paper provides an introduction and overview for the special issue on systematic conservation planning in the species-rich and highly vulnerable Cape Floristic Region. Firstly, we outline the three major problems that created the need for a systematic conservation plan and implementation programme in the region, namely an existing reserve system that is not representative of biodiversity patterns and processes, escalating threats to biodiversity, and diminishing institutional capacity. Secondly, we present the framework used for the planning and implementation process, place the contributions to the special issue in this context, and summarise current implementation initiatives. Thirdly, we extract from these studies and our own experience a number of lessons that were learnt during the planning process. Foremost amongst these lessons is a requirement for effective incorporation of implementation issues at all stages of the planning process. Other lessons include the need to consult and involve stakeholders at the local (municipal) level, the importance of a common planning framework for all teams contributing to the plan, the importance of mainstreaming biodiversity concerns as an implementation mechanism, the requirement for a critical level of home-grown capacity for undertaking ecoregional planning, and the value of expert knowledge when incorporated into a systematic planning framework. We conclude by suggesting that the approach used in this planning process, modified by accommodating the lessons learnt, has general applicability.