To determine the coral reef morpho-functional structure of San Andrés, regarding functional benthic diversity and fish (Lutjanidae), we evaluated the condition of the coral structure on the leeward side of the island, which is an area impacted by tourism, through diving and fishing. Three sampling sites were evaluated during two years recording the distribution of benthic organisms, environmental variables and Snappers density (Lutjanidae). A low density of Lutjanus jocu and Ocyurus chrysurus was found, with a high density of juveniles of L. apodus and L. mahogoni, which showed a preference for reefs with submassive and brain corals. Algae especially Macroalgae and octocorals were those with the greatest coverage in the reefs, followed by inert substrates, while corals were epresented by species with a wide distribution such as Agaricia agaricites and Porites astreoides. Octocorals correlated negatively with stony corals and that the most widespread fragile corals were the finger. We concluded that there is a higher density of mainly juvenile snappers where there is a greater variety of coral morpho-functional groups, and not necessarily in sites with greater coral coverage. Also, adult snappers were associated with octocoral zones. This shows that morpho-functional diversity is a crucial factor in the permanence of snappers.