Brazil has the most extensive and richest areas of coral reefs in the South Atlantic Ocean, with its fauna characterized by high endemism and adaptations related to its growth and morphology, to its coral building fauna and to the depositional environment that differ from other coral reefs around the world. In spite of the effects from changes in the global environmental, the main stress factors for Brazilian reefs are local level threats, such as pollution and overfishing. The effects from these threats reduce biodiversity and result in decreasing stocks at different trophic levels. The trend that currently exists, regarding marine resource use, implies that reassessing the conservation strategies is urgently necessary if the degradation of these environments is to be reversed. It is necessary that the practices used in adjacent watersheds be improved, combined with actions to protect and recover native vegetation, along with planning for developing coastal areas, which will ensure that sedimentation rates be controlled and pollution sources are drastically reduced. Brazil should have to adopt a multidisciplinary approach to lead an evolution from traditional threat management in individual portions of ecosystems to large-scale management strategies in complex socio-economic and natural systems.