Abstract Oxylipins are important signal transduction lipoxygenase-derived products of fatty acids that regulate a variety of physiological and pathological processes in plants and animals. In marine diatoms, these molecules can be highly bioactive, impacting zooplankton grazers, bacteria and other phytoplankton. However, the ultimate cause for oxylipin production in diatoms is still poorly understood, from an evolutionary perspective. Here we analysed production of particulate linear oxygenated fatty acids (LOFAs, previously named non-volatile oxylipins) from natural phytoplankton collected weekly for 1 year. We demonstrate for the first time that diatoms are the main LOFA producers in natural phytoplankton assemblages. Interestingly, LOFA-per-cell production decreased with increasing diatom density and was not due to major changes in diatom community composition. An inverse relation was confirmed at a global scale by analysing diatom lipoxygenase unigenes and metagenomes from Tara Oceans datasets. A network analysis suggested that different LOFAs could contribute to modulate co-variations of different diatom taxa. Overall, we offer new insights in diatom chemical ecology, possibly explaining the evolution of oxylipin synthesis in diatoms.