Phytoplankton samples were taken at mesophothic depths (30–150 m) over the Frijol Bank seamount inside the Corales de Profundidad National Natural Park during the dry and rainy seasons. Sixty-four forms (genera and morpho-species) of phytoplankton were found. Seasonal influence on phytoplankton assemblage structure was detected, with a number of genera preferentially associating with the dry season. Although not statistically significant, mean cell density was higher in the rainy than in the dry season whereas mean richness was the same for practical effects. Contrasting seasonal signals on phytoplankton assemblages in other Colombian Caribbean localities in comparison with the present work are discussed.