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Background The Gulf of Mexico (GOM) is a semi-enclosed sea where the waters of the United States, Mexico and Cuba converge. Al least 21 species of cetaceans inhabit it. The only mysticete (baleen whale) is found in the northeast (U.S. waters). The distribution of the 20 species of odontocetes (toothed cetaceans) is well understood in U.S. waters, but practically unknown in Mexican and Cuban waters. In this study we used sighting data from several odontocete species to construct habitat suitability maps in order to identify geographical regions suitable for high diversity throughout the GOM. Methods Historical datasets of georeferenced sightings from across the GOM were used to implement the maximum entropy algorithm (MaxEnt) to model the habitat suitability of each species. Five environmental predictors were used, selected for their influence over the occurrence of cetaceans: two oceanographic predictors (sea surface temperature and chlorophyll-a concentration), and three bathymetric predictors (depth, slope, and distance to 200-m isobath). A spatial approach based on the habitat suitability maps was used to identify the suitable regions. Results Only 12 species were modeled, which were the ones with the minimum sample size required. The models performed well, showing good discriminatory power and slight overfitting. Overall, depth, minimum sea surface temperature, and bottom slope were the most contributing predictor in the models. High suitability areas of 10 species were located on the continental slope, and four suitable regions were identified: (1) the Mississippi Canyon and the Louisiana-Texas slope in the northern GOM, (2) the west Florida slope in the east-northeastern GOM, (3) the Rio Grande slope in the west-northwestern GOM, and (4) the Tamaulipas-Veracruz slope in the west-southwestern GOM. Conclusions We were able to detect four geographic regions in the GOM where a high diversity of odontocetes is expected, all located on the continental slope. Although the methodology to identify them (spatial overlap) is a very conservative approach, it is useful for conservation and management purposes. The paucity of data did not allow all species to be modeled, which highlights the importance of establishing transboundary monitoring programs.