A biodiversity and coastal resources priority conservation site exercise is being carried out by INVEMAR in the Colombian Caribbean coast to provide information for the establishment of an effective marine protected area network. The results of the biodiversity representation and habitat heterogeneity gap analysis within the existing MPA are presented within the study. Seven “coastal systems” within the study area defined by Sullivan Sealey and Bustamante (1999) based on their drainage system, physiographic, and coastal geomorphology among other characteristics, were used as geographical planning units. Seven marine coastal habitats were also identified. The gap analysis showed that while coral reefs are very well represented in the area, sea grasses, sandy beaches, coastal lagoons, and estuaries as well as soft bottom are poorly represented. However, the enclosure percentages of each habitat within the MPA are very unequal within the different coastal systems; some habitats are represented only in one, or some times, none coastal system. The results of the study show the need of short term studies to fill information gaps such as ocean circulation, larval dispersal, fishes reproductive sites, natural tretas, and other socio-economic data in order to include these criteria into the conservation site prioritization process.