Colombia is recognized as a megadiverse country on the basis of the number of terrestrial animal and plant species occurring within its boundaries. However, due to the circumstance that it possesses coasts on both the Caribbean Sea and the Pacific Ocean, each of them exhibiting distinct geological, oceanographic, and climatic features, Colombia is perhaps the country with the highest marine biological diversity in South America and one of the most biodiverse in the New World. Although scientific research concerning marine biodiversity of Colombia has a very short history, considerable knowledge has been achieved in the last 10 years, particularly in regard to species inventories and ecosystem characterizations, including thematic mapping. Relatively accurate estimates about the numbers of species of fishes, birds, mammals, reptiles, and some marine invertebrate groups occurring in Colombian waters are now available, as well as the location, extent, and structure of the major coastal-marine ecosystems, including coral reefs, mangroves, and seagrass meadows. According to their geologic, hydrographic, climatic, and biological features, the coastal and oceanic realms of Colombia have been subdivided into 18 natural ecoregions, nine in the Caribbean and nine in the Pacific. Considering the current scientific capacity of Colombia, including financial and logistic limitations, short and mid-term research plans and programs have been designed in order to orient marine biodiversity studies toward prioritary issues and geographic areas according to the responsibilities imposed by the Biodiversity Convention and the National Biodiversity Plan.