AbstractThe protection of ecosystems with high diversity, such as coral reefs, is not an approach that guarantees their conservation. Thus, maintaining connectivity among coral populations over the long term is a strategy that should be adopted in order to protect diversity and ecological processes. Although coral reefs in Colombia are highly diverse, the population genetics baseline data of keystone species such asOrbicella faveolataare limited.To provide current information about the connectivity between populations ofO. faveolatain the Colombian Caribbean, the genetic diversity and distribution ofO. faveolatawas evaluated with analysis of molecular variance (AMOVA), principal components, and migration estimations using 113 genets distributed in six populations. Also, a genetic structure analysis that included the available data for the Caribbean population was conducted, seeking to understand how the Colombian populations relate to the broader region.According to the global fixation index (FST) for the Colombian Caribbean, there was no genetic structure (FST= 0.002). Discriminant analysis of principal components (DAPC) showed that Corales del Rosario Archipelago (CR), Este de Isla Fuerte (EIF), San Bernardo Archipelago (SB), and Varadero Reef (VR) were grouped with Oeste de Isla Fuerte (OIF), with Bushnell (BS) representing the most divergent cluster. Migration analysis showed relatively high migration from VR to CR and SB, highlighting the importance of VR as a genetic reservoir for the region. Structure analysis showed that the Colombian population presented a specific genetic identity (FST= 0.254), suggesting that the Colombian Caribbean population could be a peripheral population that contributes significantly to genetic variation and is connected through a complex connectivity process.In conclusion, the estimated genetic connectivity reflects the influence of sea surface dynamics over the interpopulation exchange dynamics and the role of protected and nonprotected coral reef in the Colombian Caribbean. Thus, the Colombian Caribbean population ofO. faveolatacould be relevant to the conservation of genetic diversity on a larger scale.