Together with phytoplankton, microphytobenthos (MPB) play an important role in the overall food web structure of coastal ecosystems by regulating nutrient fluxes, oxygen concentration and sediment stability in the ecosystem. Although there are many studies on phytoplankton, MPB dynamics in the subtidal zone are largely unknown. In this study, we carried out a whole-year survey to investigate the seasonal dynamics of phytoplankton and MPB biomass simultaneously in relation to the environmental physico-chemical parameters. We show that phytoplankton and MPB do not follow the same dynamics with MPB being the first to increase in the season. It constitutes a large energy input to the ecosystem from the beginning of spring (with 60% of the total biomass until April). The system then moves from a system dominated by benthic biomass in early spring to a system where the pelagic biomass dominates. Among resources that MPB and phytoplankton have to share, light seems to trigger the MPB bloom as soon as maximum bottom PAR is reached, i.e. one month earlier than the phytoplankton bloom in the water column. With regard to nutrients, the lack of phosphorus can be put forward to explain the decline of MPB biomass at the beginning of April, whereas the phytoplankton decline in the first week of May coincides to silicic acid deficiency. Dissolved inorganic nitrogen then becomes potentially limiting in the water column until the end of October. Competition with macroalgae at the bottom and grazing were also considered as being possible factors for the disparate course of phytoplankton and MPB dynamics. Further investigations are needed to give a more detailed picture on the interactions and feedback loops between MPB and phytoplankton. However, although benthic-pelagic relationships are complex, this study indicates the need to integrate such fundamental coupling to a thorough understanding of ecosystem dynamics and functions.