Dinoflagellates were found and seven of them are potentially toxic species Based on the CA and PCA the substrate specificity of Gambierdiscus toxicus is macroalgae Amphidiniopsis hirsutum Coolia sp and Amphidinium sp are sand Ostreopsis ovata Ostreopsis lenticularis and Prorocentrum rhatymum are seagrass sand and coral rubble Prorocentrum lima Prorocentrum emarginatum Ostreopsis siamensis and Sinophysis microcephalus are seagrass seaweed and coral rubble and Prorocentrum concavum is on all substrate Dinoflagellates were found and seven of them are potentially toxic species Based on the CA and PCA the substrate specificity of Gambierdiscus toxicus is macroalgae Amphidiniopsis hirsutum Coolia sp and Amphidinium sp are sand Ostreopsis ovata Ostreopsis lenticularis and Prorocentrum rhatymum are seagrass sand and coral rubble Prorocentrum lima Prorocentrum emarginatum Ostreopsis siamensis and Sinophysis microcephalus are seagrass seaweed and coral rubble and Prorocentrum concavum is on all substrate Dinoflagellates were found and seven of them are potentially toxic species Based on the CA and PCA the substrate specificity of Gambierdiscus toxicus is macroalgae Amphidiniopsis hirsutum Coolia sp and Amphidinium sp are sand Ostreopsis ovata Ostreopsis lenticularis and Prorocentrum rhatymum are seagrass sand and coral rubble Prorocentrum lima Prorocentrum emarginatum Ostreopsis siamensis and Sinophysis microcephalus are seagrass seaweed and coral rubble and Prorocentrum concavum is on all substrate. Research on epibenthic Dinoflagellate causing Ciguatera Fish Poisoning had been conducted in Harapan Island, Kepulauan Seribu during 4th--6th March 2013. This study was carried out by collecting seagrass, seaweed, sand, and coral rubble on the reef flats, where they were shaken vigorously to separate the epibenthic Dinoflagellates. Samples were filtered and observed under a light microscope. The data were analyzed using Correspondence Analysis (CA) and Principal Component Analysis (PCA). From the samples collected, twelve species of benthic Dinoflagellates were found, and seven of them are potentially toxic species. Based on the CA and PCA, the substrate specificity of Gambierdiscus toxicus is macroalgae; Amphidiniopsis hirsutum, Coolia sp., and Amphidinium sp. are sand; Ostreopsis ovata, Ostreopsis lenticularis, and Prorocentrum rhatymum are seagrass, sand, and coral rubble; Prorocentrum lima, Prorocentrum emarginatum, Ostreopsis siamensis, and Sinophysis microcephalus are seagrass, seaweed, and coral rubble; and Prorocentrum concavum is on all substrate.