In 2011, shallow marine ecosystems were evaluated (0-30 m depth) in the oceanic reef complexes in the northern Colombian Caribbean, including New Shoal, Alice Shoal (Colombia-Jamaica Joint Regime Area) and Serranilla Bank, in the Seaflwer Biosphere Reserve. Sampling stations were defied a priori through visual analysis of satellite images. Ecological Rapid Assessments were conducted to record the composition and relative abundance of the most representative species and groups existing in each oceanic shoal (hard corals, macroalgae, sponges, octocorals, macroinvertebrates, seagrass beds, and fihes). The greatest number of species was registered in Serranilla Bank (341), followed by New Shoal (242) and Alice Shoal (122). Fishes were the most representative group with 135 species. Seven exclusive species were found in Alice Shoal, 42 in New Shoal and 128 in Serranilla Bank. 18 species were registered with endangered categories at a global and national level, three of which (Gorgonia ventalina, Ginglymostoma cirratum and Balistes vetula) were found in important proportions. Species richness and the diversity of marine ecosystems found in this study highlight the importance of these remote areas as reserves of biodiversity in the Colombian Caribbean.