Jet-loop reactors (JLR) used as biological waste treatment processes introduce an additional selective pressure on the natural microbial flora of the incoming effluent. Several high-performing microbial inocula were tested for winery wastewater treatment and the microbial composition was analysed. A microbial consortium was enriched and selected for use with a new type of aerobic JLR. The reactor was operated continuously for more than 1 year using winery wastewaters collected in different seasons. Chemical oxygen demand (COD) removal efficiency was on average greater than 80%, with retention times of 0.8-1 day. Microbial populations were sampled for characterisation after 6 months and at the end of the study. Isolates were identified at genus and/or species level. Almost all isolates belonged to the genera Pseudomonas and Bacillus. Saccharomyces cerevisiae was also found but no filamentous fungi. These results show that a highly adapted population develops in JLRs treating winery effluents as compared to other bioreactors. Aerobic JLRs impose a stringent selective criterion on the composition of the microbial biomass.