This chapter focuses on the management of protected areas in the Amazon basin. Rivers serve as natural barriers for the distribution of biodiversity and in the Amazon, caused the development of two different types of ecoregions where species evolve in different directions. The justification for establishing a protected area is centered in the presence of a unique biodiversity and sustainable use of natural resources by a traditional population. There are two types of protected areas: those such as national parks or biological reserves, in which traditional populations are not permitted to live inside and natural resources are not permitted to be used, and sustainable use units, in which traditional populations can live and use resources. These are managed by units above the unit itself, such as mosaics of conservation units. All conservation units are protected areas, but not every protected area is a conservation unit.