Marine biodiversity in French Guiana is strongly influenced by the amagon River waters of the river Amazon, which constitute a major structuring factor for the estuarine, coastal, and shelf marine ecosystems. Moreover, the marked seasonal and interannual variabilities play important roles in the stability or fluctuations in the environmental parameters that influence biodiversity at the ecological, population, and genetic levels. Previous and ongoing studies of the marine and littoral biota relate mostly to commercial marine species, protected species in danger of extinction and, specially, to the biodiversity and functioning of local coastal and littoral ecosystems such as estuaries, mudflats, sandy beaches and, particularly, littoral mangroves. A more integrated approach involving local, regional, and international scientific collaboration is needed for a better assessment and understanding of marine biodiversity. Such studies would benefit from international cooperation that would allow the gathering of new information and the comparison of previous data, the organization of common oceanographic surveys, the homogenisation of analytical protocols, and also favour the exchange of scientists and postgraduate students for a real transfer of ideas, techniques, and know-how. Moreover, research on the comparative biodiversity of analogous littoral and marine ecosystems in different parts of South America would allow a more accurate estimate of marine biodiversity on a continental scale.