The proliferation of bacteria in intensive aquaculture systems may be responsible for poor growth and mass mortality of marine fish larvae. Essential fatty acids provided in the diet could protect larvae by modulation of the immune response via arachidonic acid (AA) and eicosapentaenoic acid (EPA). Winter flounder Pseudopleuronectes americanus larvae were fed rotifers Brachionus plicatilis enriched with three commercial diets containing different fatty acid profiles. Bacterial colonization on the gills and skin and in the intestinal lumen was evaluated at the end of the rotifer feeding period (day 26), and growth was surveyed until metamorphosis. At 26 days post hatching, larvae fed rotifers containing the higher AA content and with a higher docosahexaenoic acid (DHA) to EPA ratio showed better growth and the lowest bacterial colonization of the intestinal lumen compared to larvae fed rotifers with the lowest AA and DHA : EPA levels. AA had been selectively incorporated into the polar lipids of larvae fed the rotifers enriched with the three diets. This is the first study in winter flounder larvae to report a link between different commercial rotifer enrichments and bacterial density in intestinal lumen.