Diatoms are unicellular plants broadly present in freshwater and marine ecosystems, where they play a primary role in sustaining the marine food chain. In the last 10 years, there has been accumulating evidence that diatoms may have deleterious effects on the hatching success of zooplankton crustaceans such as copepods, thus affecting dynamics of planktonic populations and limiting secondary production. At the molecular level, failure to hatch is ascribed to the presence of a family of inhibitory oxylipins, which we propose to collectively name polyunsaturated short-chain aldehydes (abbreviated here as PUSCAs). Here we describe the origin of PUSCAs produced by the marine diatom Skeletonema costatum via a lipoxygenase-mediated pathways involving non-esterified polyunsaturated fatty acids (PUFA). Experiments with complex lipids proved the pivotal role of chloroplast-derived glycolipids, especially monogalactosyldiacylglycerol (MGDG), in providing hexadecatrienoic acid (C16:3 omega-4), hexadecatetraenoic acid (C16:4 omega-1) and eicosapentaenoic acid (C20:5 omega-3) to the downstream process leading to 2E,4Z-octadienal (C8:2 omega-4), 2E,4Z,7-octatrienal (C8:3 omega-1) and 2E,4Z-heptadienal (C7:2 omega-3), respectively. Under physiological conditions, the hydrolytic process is associated to galactolipid hydrolyzing enzyme capable of removing fatty acids from both sn positions of glycerol.