Brazil has one of the highest biodiversities in the world, both in the terrestrial and the marine environment. Thanks to its extensive coastal line, Brazilian marine flora and fauna are composed of species from many different marine bioregions. The ecosystems on the south-eastern and southern coasts have received considerable attention but, due to the great impact of human activities such as tourism, over-exploitation of marine resources, physical alteration, oil related activities and pollution among others, this environment is under great risk and its biodiversity is threatened. The most representative ecosystems of this region include sandy beaches, rocky shores, sea grass beds, soft bottom communities and mangrove forests. On the northern coast where the Amazon reaches the ocean, there is a complex group of freshwater, estuarine and marine ecosystems; the habitats there are very diverse and poorly known. This paper summarizes the known, which is the information currently available in Brazil in various types of publications resulting from research in marine biodiversity and the different ecosystems. As the unknown, a research priority is proposed involving the completion of a list of species and an assessment of the state of health of the main ecosystems on a national scale. This new information will need to be integrated and summarized in countrywide Geographic Information System (GIS) databases, accessible to the scientific community as well as to the management agencies. In the long-term, a genetic inventory must be included in order to provide better knowledge of the biological resources. Possible future projects at the local (Brazil), regional (Atlantic, off South America) and global (the whole of South America) scale are envisaged.