Genetic connectivity was studied in two scleractinian corals, Pocillopora damicornis (branching and broadcast spawner) and Pontes panamensis (massive and brooding type), along the Pacific coast of Mexico. Allelic diversity between adults and juveniles, the latter recruited after the El Niño—Southern Oscillation (ENSO) 1997–1998 event, was determined, and level of genetic connectivity among populations was assessed. There were no significant differences in allelic diversity between adults and juveniles from the same location. Seascape spatial genetic analysis suggested two or three clusters, depending on the species: (1) Bahías de Huatulco, (2) south of the Baja California Peninsula and Bahía de Banderas, and (3) locations in the Gulf of California. The most important barrier to gene flow was detected between Bahía de Banderas and Bahías de Huatulco and corresponds with a major coastal stretch of sandy beaches and lagoons. Moderate to high gene flow was found inside and at the entrance of the Gulf of California (N_em = 62–250), possibly favored by seasonal circulation patterns and sexual reproduction. In contrast, low gene flow was observed between southern populations and the rest of coastal Mexico (N_em < 1.7) based on high local recruitment and habitat discontinuity. A close genetic relationship of corals from the southern part of the Baja California Peninsula and severely damaged Bahía de Banderas coral communities confirmed that exchange of propagules could have taken place between the localities after the ENSO 1997–1998 event. Despite different reproductive strategies, both species showed similar patterns, suggesting the importance of surficial currents and habitat discontinuity to predict connectivity among coral reefs.