In the context of populations, connectivity has been defined as the link existing among organisms of the same species located in different zones of their distribution range, determined by the exchange of larvae, recruits, juveniles or adults. The concept of connectivity became important when the fragmentation of habitat was considered a threat to biodiversity. The ideas of fragmentation and connectivity have been largely focused on terrestrial areas, particularly highly fragmented temperate forests, so one of the challenges for modern research is to broaden the prospects for determining connectivity in less fragmented habitats as well as in water environments, both fresh or salty. Our research has been focused on marine organisms of Mexican reef systems; both molecular biology methods and purely ecological analyses have been used to infer connectivity patterns. Several results have been derived from these investigations, among which we can highlight the evidence that the Mexican Caribbean (CM) reef systems could be considered centers of biodiversity in relation to those of the Veracruzan Arrecifal System (SAV), furthermore has been settled that there is limited genetic connectivity between both systems so that the SAV reefs could be highly susceptible to environmental stress. In addition, in a recent study on the connectivity patterns of the grey snapper (Lutjanus griseus), a species of commercial importance in the Mexican Caribbean, it has been possible to determine that the subpopulations studied form a metapopulation, so that the fishery of L griseus has not impacted on genetic connectivity in Quintana Roo. Finally, it is important to mention that it was detected that reef areas (Punta Herrero and Xahuayxol) had the highest values of genetic diversity among all the studied sites.