The year 2000 marks 500 years of massive destruction for the Brazilian Atlantic Forest, as a consequence of the European colonization of Brazil. Today, the Atlantic Forest is restricted to ca 98,800 km² of remnants, or 7.6 percent of its original extension. The Atlantic Forest continues to suffer under severe anthropogenic pressure, risking imminent extinction of the remaining species. Our current knowledge indicates that this complex biome contains a species diversity higher than most of the Amazon forests, and also has high levels of endemism. The 13 selected articles in this special issue present data on the natural history, ecology, sustainable management, and conservation of the Atlantic Forest. These articles represent a sample of the research conducted to date in the region and suggest avenues of future research, particularly with regard to conservation alternatives for the remaining portions of the Atlantic Forest. This special issue represents one of the first general references pertaining to the Brazilian Atlantic Forest.