The populations of Acropora palmata have decreased over the last four decades, and although there are several studies on their genetic diversity in the Caribbean, no studies have been published about the reefs from the southern Gulf of Mexico. This research aimed to determine, using five microsatellite markers, the genetic variation of three A. palmata populations in the Mexican Atlantic located in the southwest Gulf of Mexico, in the Campeche Bank, and in the Caribbean. The mean of genetic richness (Ng/N) in the studied reefs was 0.583; the lowest estimated value corresponded to the Campeche Bank reef. A low genetic diversity was registered in the studied reefs (reef mean He = 0.315 ± 0.052). The significant genetic structure observed among studied populations could be related to ocean currents from the region and specific biological characteristics, mainly, short larvae phase, high mortality, and high rate of self-recruitment. These results may be particularly useful for designing management strategies, considering the lack of studies of this type in the region.