Todos os Santos Bay is a Brazilian Environmental Protection Area equivalent to Category V of the International Union for Conservation of Nature, which encloses two groups of coral reefs in the region of the greatest biodiversity in the Western South Atlantic Ocean, the coast of the state of Bahia. This type of Protected Area aims the sustainable use of the natural resources and the biodiversity conservation. The Todos os Santos Bay Environmental Protection Area does not have a management plan, yet, that is a tool for restricting the use of natural resources in order to promote conservation of the environment. In Todos os Santos Bay there are two regions of reefs with different hydrodynamic regimes and human impacts: the reefs located at the entrance of the bay, the outside reefs, which are directly exposed to the wave’s action, and the largest group of reefs that is located inside the bay in a lower hydrodynamic regime. These later reefs are located near Salvador, a city with 2.8 million inhabitants and of an industrial center, with a history of more than 40 years of pollution. Nowadays, dumping of both domestic and industrial wastewater has decreased, although much still needs to be improved, and the area of environmental protection can be an important legal tool to this purpose. This study aims to determine whether the differences between these two groups of reefs regarding the macrobentonic and coral communities justify the creation of an independent No Take Zone for each group. Twenty three stations were sampled, eight in the outside reefs and fifteen in the inside reefs, all during scuba diving, applying the video-transect technique, along six transects per reef station, each 20 m long and 0.21 m wide. Due to limitation of this technique for identifying species with low abundance, sampling was complemented with visual identification of all species of corals in each reef station. The video-transect images were analyzed in the free software VITRA with 20 points per frame. Three matrices were generated, one of the macrobentonic community structure, the second one of the coral community structure and one third of the coral community composition. The qualitative matrix generated by the visual identification of corals was better for the coral species distribution than the quantitative one generated by the video-transect. Differences between the two reef groups were tested with the analysis of similarity. In order to quantify the differences it was used the similarity percentage, and for the graph representation the multi- dimensional scaling. Because the matrices of the macrobentonic and the coral community structures are compose of the same set of data, generated by the analysis of the video-transects, the alpha was adjusted for Bonferroni correction from 0.050 to 0.025. However, for the coral community composition, the alpha was maintained in 0.050 because these data come from the visual identification in the field. The results were significant for both, the coral community structure and the coral community composition. The reefs located at the entrance of the bay are differentiated by the highest abundance of the incrusted and articulated calcareous algae. The most abundant species of corals are the ones belonging to the complex Siderastrea and the species Mussismilia hispida, M. braziliensis and Porites branneri. The reefs located at the interior of the bay have a higher abundance of corals and sponges. The dominant coral specie is Montastraea cavernosa, but the hydrocoral Millepora alcicornis and the Siderastrea complex are very abundant as well. These differences are significant and justify the creation of two independent no take zones in order to protect the peculiarities of each reef group. The results of this study were given as suggestions to the team that is preparing the Todos os Santos Bay management plan, along with the suggestion for creating two No Take Zones.