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In the last decades, harmful algal blooms (HAB) and toxic events such as ciguatera seem to have increased in frequency and intensity, negatively impacting human health, economy, and marine ecosystems. In Colombia, these events have caused a series of consequences ranging from the death of fish and birds to toxic effects on humans. Although some toxin-producing dinoflagellate species are common in the Caribbean, their dynamics are poorly understood, making the adoption of any regulations difficult. To determine the composition and abundance of dinoflagellates associated with seagrasses we collected 18 samples on Isla de Baru, during 2015. We found ten diatom genera and three dinoflagellate genera, Prorocentrum, Ostreopsis, and Gambierdiscus, that include toxigenic species related to ciguatera and diarrheic shellfish poisoning. Prorocentrum lima was the most abundant dinoflagellate, with average cell densities of 52 +/- 48 cells/g substrate wet weight. The temperature hypothesis gains strength as one of the main modulators of dinoflagellate abundance observed in the Caribbean, especially regarding Prorocentrum species and some diatoms such as Mastogloia corsicana and Actinocyclus normanii. This assumption is supported by the Since high positive correlation between EI Nino Southern Oscillation and the sea surface temperature in the Caribbean during 2015.