Mesophotic coral ecosystems (MCE) are located between 30 and 150 m deep and shelter unique communities. However, they have been poorly studied due to the high cost of the available sampling technologies. Zooplankton are key organisms for the maintenance of the coral colonies as their primary food source because the zooxanthellae in these habitats have a low photosynthetic rate due to the low light incidence. The purpose of this work was to characterize the zooplankton community associated with MCEs. We took 15 samples (three samples per station) by filtering 24 L of seawater (45 µm mesh size) in five stations at Bajo Fríjol with a device designed to collect zooplankton right just above the reef substrate. We determined the taxonomic composition, density, and relative abundance, and we categorized the species according to their trophic level. Crustaceans (especially nauplii and copepods), tintinnids, and foraminifers were the most abundant while tintinnids and radiolarians had the higher species richness. Herbivores dominated in both composition and abundance as usually happens in other pelagic communities. We present here the first reports of planktonic radiolarians and tintinnids from oceanic zones and MCEs in the Colombian Caribbean and the first global list of zooplankton species associated with MCEs.