To map ecological units in mesophotic coral ecosystems on the western side of San Andrés Island (Colombia) considering biotic components and geomorphic zonation among 30–140 m deep, 27 video transects were done using an ROV. In total, 14 h of video were recorded and 5742 still images were extracted from them, from which 753 met quality criteria for bottom coverage and organisms’ abundance estimations. These estimates were calculated from images through the Planar-Point Intercept method (PPI) using a 1 m × 0.5 m quadrant gridded 0.1 m × 0.1 m. CLUSTER, SIMPROF, and SIMPER analysis of benthic composition considering depth ranges in the group’s formation were done. The clusters formed were simplified and generalized using a color matrix to support the mapping process. Two geomorphological units were found, the deep reef terrace (30–60 m) and the reef slope (60–357 m), overlapping with five ecological units spanning 268 ha. The units Bioturbed sediments–Calcareous algae, Octocorals–Mixed corals, and Octocorals–Sponges sited on the deep reef terrace have been previously described in the shallow waters of the island, and the units Octocorals–Sponges–Antipatharians and Encrusting Sponges sited on the reef slope are described as new here. These findings contribute to the knowledge of Caribbean mesophotic coral ecosystems and are useful to update the Colombian coral reef atlas.