Intermediates of the aldehyde biosynthesis in Thalassiosira rotula are investigated. Use of labeled precursors and cell preparations proves production of 2E,4Z-octadienal from 6Z,9Z,12Z-hexadecatrienoic acid (C16:3 omega-4) through the lipoxygenase-dependent intermediate (9S)-9-hydroperoxyhexadeca-6,10,12-trienoic acid. On the contrary, synthesis of 2E,4Z,7Z-decatrienal involves mainly EPA (C20:5 omega-3) by a 11R-lipoxygenase, as suggested by identification of chiral 11R-HEPE (12% e.e.) in the diatom extracts. Consistently with the necessity to have a rapid transport and metabolization of the intermediate hydroperoxides, we show that lipoxygenase and lyase activities are both found in the same subcellular fraction of the microalga.