Harmful and non-harmful dinoflagellates in the Pelican Cays coral reef ecosystem were examined, in an archipelago of mangrove islands situated on the top of an atoll-like coral reef, in the center of southern Belize barrier-reef lagoon. Mangrove fringed ponds in the Pelican Cays supported rich dinoflagellate populations. The six pond habitats selected were distinctive in its dinoflagellate species composition. Manatee Cay and Douglas Cay were the most species rich, with an unusual high number of oceanic species, whereas Elbow Cay exhibited benthic species. In Manatee Cay the taxa included 13 Protoperidinium spp., and 9 Ceratium spp.; in Douglas Cay 8 Protoperidinium spp. and 4 Ceratium spp.; and in Douglas Cay 7 Gonyaulax spp. and 3 Prorocentrum spp. The taxa of harmful species was the highest in the Manatee Cay: 5 Prorocentrum spp., 4 Ostreopsis spp., 3 Dinophysis spp., 3 Gambierdiscus spp. and 1 species each in the following genera: Amphidinium, Cochlodinium, and Gonyaulax, whereas the lowest number of species were in Lagoon Cay: Gambierdiscus toxicus, Prorocentrum hoffmannianum and Pyrodinium bahamense var. compressum, respectively. The Pelican Cays posses a diverse dinoflagellate assemblages of oceanic, planktonic, and benthic species including harmful species and provide important habitats for shallow-water microscopic flagellates.