Understanding how populations are inter-connected can help identify species that are vulnerable or those that are likely to persist over ecological and evolutionary time scales. Favia fragum and Favia gravida are sister species of brooding corals common in the Atlantic Ocean that are secondary reef-builders that contribute to habitat complexity in intertidal and shallow-water coral reefs. To better understand population connectivity in these two congeneric species with broad and presumably non-overlapping distributions, one single-copy nuclear marker (masc1) and one ribosomal marker (ITS) were used to estimate population genetic parameters for Favia in four biogeographic regions: the Caribbean, Brazilian, Ascension and Tropical Eastern Atlantic provinces. Strong and significant levels of population structure were found among all four biogeographic regions, with each province being characterized by nearly all private alleles. Phylogenetic analyses based on each gene and on a combined marker analysis showed strong support for three sister clades composed of individuals from either the Caribbean, South Atlantic (Brazilian + Tropical Eastern Atlantic), or Ascension provinces. However, low genetic diversity was observed at each location, and no differentiation was observed among populations along the entire coast of Brazil (~ 1600 km). Furthermore, the Tropical Eastern Atlantic was likely colonized by at least two independent founder events, one from the Caribbean and another from the Brazilian provinces. Life-history traits of the genus might explain the different patterns found. Favia fragum and F. gravida release zooxanthellae larvae monthly and may be capable of rafting, which could favor occasional long-distance dispersal. On the other hand, they are capable of self-fertilization and commonly disperse over a few meters which may explain low genetic variability locally. Our results show that while long-distance migration events are possible for Favia corals, they are insufficient to maintain connectivity across biogeographic regions. Lastly, the Ascension Island population was more divergent than the sister clades composed of Caribbean or South Atlantic Favia, indicating a possible cryptic lineage, but further work may clarify species boundaries within the Atlantic coral genus Favia