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The accumulation of bacteria in Brachionus plicatilis and Artemia franciscana during a short-term incubation was quantified using immunocolony blot (ICB) and an enzyme-linked immunosorbent assay (ELISA). Four bacterial strains, isolated from turbot and halibut, were grazed effectively by both species when given at high concentrations (≥5×10 7 bacteria ml −1 ). B. plicatilis accumulated 21–63×10 3 bacteria per rotifer and A. franciscana up to 45×10 3 bacteria per metanauplius after 20–60 min of grazing. The composition of the bacterial microflora of the live food organisms changed drastically, as the bioencapsulated strains comprised up to 100% of the total count of colony-forming units. After incubation in the bacterial suspensions, B. plicatilis and A. franciscana were transferred to seawater with added microalgae ( Tetraselmis sp., 2 mg C l −1 ), to evaluate the persistence of the changed bacterial composition in conditions similar to those present in a first feeding tank. The bioencapsulated bacteria decreased in numbers, but in most cases remained present in both live food organisms after 24 h. It is possible, after a short-term incubation, to replace opportunistic (r-selected) bacteria present in the live food cultures with other bacteria, which persist as a dominant part of the bacterial flora of the live food for a relatively long period of time (4–24 h).