Venezuela is among the ten countries with the highest biodiversity in the world, both in the terrestrial and the marine environment. Due to its biogeographical position, Venezuelan marine flora and fauna are composed of species from very different marine bioregions such as the Caribbean and the Orinoco Delta. The ecosystems in the Caribbean have received considerable attention but now, due to the tremendous impact of human activities such as tourism, over-exploitation of marine resources, physical alteration, the oil industry, and pollution, these environments are under great risk and their biodiversity highly threatened. The most representative ecosystems of this region include sandy beaches, rocky shores, seagrass beds, coral reefs, soft bottom communities, and mangrove forests. The Orinoco Delta is a complex group of freshwater, estuarine, and marine ecosystems; the habitats are very diverse but poorly known. This paper summarizes the known, which is all of the information available in Venezuela about research into biodiversity, the different ecosystems and the knowledge that has become available in different types of publications, biological collections, the importance and extents of the Protected Areas as biodiversity reserves, and the legal institutional framework aimed at their protection and sustainable use. As the unknown, research priorities are proposed: a complete survey of the area, the completion of a species list, and an assessment of the health status of the main ecosystems on a broad national scale. This new information must be integrated and summarized in nationwide Geographic Information Systems (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 more detailed knowledge of the biological resources. Future projects at the local (Venezuela), regional (Southern Caribbean: Colombia, Venezuela, and the Netherlands Antilles), and global (South America) scales are recommended.