The International Census of Marine Microbes (ICoMM), together with the South American and Caribbean Steering Committees of the Census of Marine Life program (CoML), supported the initiative of launching a regional lCoMM node (LACar ICoMM). This network aims at promoting discussions among scientists currently involved in marine microbial studies carried out at both the South American and the Caribbean regions, in order to evaluate the research capabilities and to identify complementary strengths and/or possibilities for enhanced collaboration, that would improve the knowledge on marine microbes and their biodiversity in both regions. We present an overview and discussion on some of the directions of current research on marine microbes in these regions. Concerning the marine phytoplankton studies, the best known taxonomic groups are diatoms and dinoflagellates. In Mexican marine waters, the number of taxa recorded to date is of about 1400. Studies dealing with bacterial, phytoplankton and/or cyanobacterial dynamics are carried out in the Caribbean coastal and oceanic marine systems, underscoring the importance of various environmental states, modulated by geographic and seasonal patterns as well as by the expression of large South American rivers. One of the main issues of this type of survey is the determination of wet and dry seasonal patterns of bacterial dynamics, in seascapes off Puerto Rico, with moderate to absent river inputs. Phytoplankton and bacterioplankton dynamics are also studied in F. Guiana coastal and shelf systems under direct Amazon influence, well known for their important fisheries resources, as well as in other South American marine systems influenced by important fresh water inputs or under upwelling conditions. Bacterial and/or picoeukaryotes diversity are assessed in particular marine systems such as coastal lagoons in Uruguay, the Rio de la Plata estuary and adjacent areas, as well as in sediments of the Oxygen Minimum Zone (OMZ) off South American Pacific coast, and in anoxic waters of the Cariaco Basin. Findings of a diverse range of pico-autotrophs (Patagonian shelf) and particular communities of big filamentous bacteria (OMZ zone off the South American Pacific) represent recent discoveries in those areas. In polluted coastal systems, bacteria with ability to degrade pesticides and hydrocarbons are currently monitored. In coastal areas of the Colombian Caribbean, 64 native marine bacterial strains were isolated from sediment samples. The oil-degrading bacteria are also studied in the Orinoco Delta, submitted to intensive oil exploitation. Furthermore, the Microbial Observatory of Rio de Janeiro (MoRio) established in Guanabara Bay (Brazil), constitutes a model for the study of threatened tropical coastal systems by exploring microbial biodiversity in different coastal systems (including unpolluted sites). The estimation of the activity and diversity of hydrocarbon and oil-degrading bacteria is assessed also in temperate waters and sediments of coastal systems of Argentina. Sharing knowledge and capabilities in common strategies would allow a better understanding of marine microbial diversity patterns in both regions. Rev. Biol. Trop. 56 (Suppl. 1): 183-214. Epub 2008 May 30.