The future of life on Earth depends on how the ocean might change, as it plays an important role in mitigating the effects of global warming. The main role is played by phytoplankton. Not only are phytoplankton the base of the oceans’ food web, but they also play an important role in the biological carbon pump (BCP), the process of forming organic matter (OM) and transporting it to the deep sea, representing a sink of atmospheric CO2. Lipids are considered important vectors for carbon sequestration. A change in the phytoplankton community composition as a result of ocean warming is expected to affect the BCP. Many predictions indicate a dominance of small at the expense of large phytoplankton. To gain insight into interplay between the phytoplankton community structure, lipid production and degradation and adverse environmental conditions, we analyzed phytoplankton composition, POC and its lipid fraction in the northern Adriatic over a period from winter to summer at seven stations with a gradient of trophic conditions. We found that at high salinity and low nutrient content, where nanophytoplankton prevailed over diatoms, the newly fixed carbon is substantially directed toward the synthesis of lipids. Lipids produced by nanophytoplankton, coccolithophores and phytoflagellates, are more resistant to degradation than those produced by diatoms. The difference in lipid degradability is discussed as a difference in the size of the cell phycosphere. We hypothesize that the lipids of nanophytoplankton are less degradable due to the small phycosphere with a poorer bacterial community and consequently a lower lipid degradation rate compared to diatoms. The lipid chemical composition of the different phytoplankton groups could have a different susceptibility to degradation. Results suggests a successful lipid carbon sink of nanophytoplankton and thus a negative feedback on global warming.