Abstract The temporal distributions of microphytoplankton were studied monthly over 2 years in the shelf and the offshore waters of the “low nutrients low chlorophyll” (LNLC) southeastern (SE) Mediterranean Sea. The microphytoplankton were comprised mostly of diatoms (0–542 cells L−1, ~4 × 106–44 × 106 cells m−2) of the genera Rhizosolenia, Thalassionema, Chaetoceros, Leptocylindrus and Pseudo-nitzschia, and dinoflagellates (1–89 cells L−1, ~1 × 106–10 × 106 cells m−2) of the genera Tripos (formally known as Ceratium), Ornithocercus, Protoperidinium, Ceratocorys and Dinophysis. During the winter mixing, microphytoplankton abundance was ~2-fold higher than during the stratified summer months, in accordance with the higher inorganic nutrient levels. Diatoms were mostly found in the upper illuminated layers (0–100 m), while dinoflagellate distribution was patchy and spread from surface down to 200 m. We also calculated that diatoms and dinoflagellates contribute negligibly (~4%) to the total vertical carbon flux in the offshore water, suggesting fast recycling of organic matter at the photic layer. Our results provide a baseline to better understand carbon and biogenic silica fluxes at the LNLC SE Mediterranean Sea.