Mesophotic coral ecosystems (MCEs) in Puerto Rico cover a potential area of 2180 km2 or 38% of the total area from the shoreline to 150 m. MCEs occur primarily along the upper insular slope of the Puerto Rico-Virgin Islands platform. Patchy MCE development occurs along the insular slope, with distribution strongly related to geomorphology. Shallow mesophotic platforms can support well-developed coral communities dominated by the Orbicella annularis species complex, but deep mesophotic platforms are more poorly developed and consist primarily of algae and sponges, with patchy occurrences of corals, dominated by Agaricia spp. Macroalgae, with 185 taxa, are the dominant component of MCEs, both in species richness and percent cover. The dominant algal components below 40 m are calcified encrusting red algae including Corallinales and Peyssonneliales species. Twenty-seven scleractinian corals and two hydrocorals were recorded within MCEs. Dominant corals in shallow MCEs were Orbicella spp., Siderastrea siderea, and Porites astreoides, but by 50 m Agaricia dominates, particularly A. undata, A. lamarcki, and A. grahamae. Over 100 fish species have been recorded from mesophotic depths, with Chromis insolata being the most common and abundant species. High vertical connectivity appears to occur within fishes, with a significant component potentially dependent on shallow, nearshore nursery areas. For all taxa, species richness and abundance decreased with depth, and changes in community structure were observed, with noted breaks occurring at ~45 and ~60 m. Primary local threats to Puerto Rico’s MCEs are overfishing, invasive species, and land-based anthropogenic inputs that increase turbidity and sedimentation.