In the period 2001–2003, I quantitatively explored the importance of mixotrophic and heterotrophic dinoflagellates in four eutrophic gulfs on the Greek coastline of the Aegean Sea, eastern Mediterranean. Phytoplankton analysis (250 samples, 401 species) focused on determinations of cell abundance and carbon biomass of diatoms, dinoflagellates (autotrophic, mixotrophic, heterotrophic), and coccolithophores. Among the 177 dinoflagellates, 145 autotrophic, 18 mixotrophic, and 14 heterotrophic species were identified comprising up to 18%, 3%, and 1% of total phytoplankton cell abundance, respectively. Analysis of total carbon biomass contributions among taxa showed that the heterotrophic dinoflagellate population contributed the highest carbon proportion (65%) to the stocks of phytoplankton community in contrast to the low contributions of the autotrophic (14%) and mixotrophic (1%) dinoflagellate species. One heterotrophic and 11 mixotrophic species were harmful algae. This major contribution of heterotrophic species to total carbon biomass may affect the concepts of trophodynamics and food web structure. Seasonal and regional distributions of heterotrophic and mixotrophic dinoflagellates are considered.