Aims:  To evaluate the effect of Vibrio harveyi strains on the growth rate of the gnotobiotically cultured rotifer Brachionus plicatilis, and to establish whether quorum sensing is involved in the observed phenomena. Methods and Results:  Gnotobiotic B. plicatilis sensu strictu, obtained by hatching glutaraldehyde‐treated amictic eggs, were used as test organisms. Challenge tests were performed with 11 V. harveyi strains and different quorum sensing mutants derived from the V. harveyi BB120 strain. Brominated furanone [(5Z)‐4‐bromo‐5‐(bromomethylene)‐3‐butyl‐2(5H)‐furanone] as a quorum sensing inhibitor was tested in Brachionus challenge tests. Some V. harveyi strains, such as strain BB120, had a significantly negative effect on the Brachionus growth rate. In the challenge test with MM77, an isogenic strain of BB120 in which the two autoinducers (HAI‐1 and AI‐2) are both inactivated, no negative effect was observed. The effect of single mutants was the same as that observed in the BB120 strain. This indicates that both systems are responsible for the growth‐retarding (GR) effect of the BB120 strain towards Brachionus. Moreover, the addition of an exogenous source of HAI‐1 or AI‐2 could restore the GR effect in the HAI‐1 and AI‐2 nonproducing mutant MM77. The addition of brominated furanone at a concentration of 2·5 mg l−1 could neutralize the GR effect of some strains such as BB120 and VH‐014. Conclusions:  Two quorum sensing systems in V. harveyi strain BB120 (namely HAI‐1 and AI‐2‐mediated) are necessary for its GR effect on B. plicatilis. With some other V. harveyi strains, however, growth inhibition towards Brachionus does not seem to be related to quorum sensing. Significance and Impact of the Study:  Interference with the quorum sensing system might help to counteract the GR effect of some V. harveyi strains on Brachionus. However, further studies are needed to demonstrate the positive effect of halogenated furanone in nongnotobiotic Brachionus cultures and eventually, in other segments of the aquaculture industry.