The multi‐temporal and spatial scale interaction of history, geography, and evolution are responsible for Colombia's extreme diversity. This chapter first describe Colombia's biological complexity and its conservation context. Then, it presents some of the main challenges for conservation professionals, managers, and decision makers in their aim to preserve Colombia's rich biodiversity for generations to come. These challenges for biodiversity conservation in Colombia are divided into two categories: (1) territorial issues and current development models; and (2) threats specific to the different ecoregions. In addition, the challenges associated with conservation strategies, specifically the creation and management of protected areas (PAs) and ecological restoration are discussed.