Biofilms in aquaculture facilities are potential reservoirs of detrimental bacteria which can affect the health of cultured animals. Procedures to control biofilm development, such as ozonation, may prove important towards commercially viable aquaculture strategies. The effect of seawater ozonation on biofilm formation and community structure was investigated with flurescence in situ hybridization (FISH) and denaturing gradient gel electrophoresis (DGGE) in small-scale aquaculture rearing tanks containing the brine shrimp Artemia. It was found that seawater ozonation accelerated bacterial reproduction and the biofilm formation cycle. Ozonation however delayed the establishment of filamentous bacteria, which may prove beneficial where filamentous biofouling of culture animals is of concern. FISH and DGGE showed distinct modifications of the community structure after ozonation. The biofilm in tanks receiving ozonated water was dominated by Gammaproteobacteria (21-65% of cells detected with EUB338), whereas it comprised mainly Alphaproteobacteria (20-50%) in tanks receiving non-ozonated water. Cytophaga-Flavobacteria and Planctomycetes constituted up to 18% within non-ozonated water but less than 10% within ozonated water. DGGE bacterial fingerprints from two time points indicated a successive change in the dominant biofilm populations within both water types. Although the used ozonation conditions did not hinder biofilm formation, improved Artemia survival rates in tanks receiving ozonated water suggest that the effects of seawater ozonation on bacterial populations may prove favourable for animal survival in aquaculture systems. In conclusion, the results suggest ozonation as a promising approach for the manipulation of bacterial populations and the restriction of detrimental bacteria in aquaculture systems.