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Microbiota was studied in 20-day old seabass larvae after 10 days of feeding compound diets, in comparison with a control group kept live food. This early weaning caused bacterial overload in the larvae fed the normal compound diet (109 CFU per g of body weight). The bacterial load was significantly limited with a diet lacking ferrous salt in the mineral premix (3 × 108 CFU g−1). A similar range of associated flora was observed before weaning at day 10, but only 107 CFU g−1 were counted in the larvae fed Artemia till day 20. The bacterial surge in weaned larvae was due to one strain of Vibrio, especially dominant in the iron-supplemented diet. In spite of its opportunism, the strain did not seem pathogenic to starving seabass larvae challenged from day 5 to day 10. This Vibrio produced siderophore, protease, phospholipase and amylase. These extracellular products were also produced by 25 to 60% of the diversified flora of the Artemia-fed larvae. Lipase was the main extracellular product observed in the latter flora (80% of the isolates), whereas it was seldom produced in the weaned groups (less than 10%). The omission of dietary ferrous salt had no detrimental effect on survival and growth rates of the larvae, but limited bacterial load. It is concluded that diet formulation should take into account the effects on microbiota, based on this first example with iron limitation.