Polyhydroxyalkanoates (PHAs) are interesting as material for bioplastic production because they are recognized as biodegradable and could be produced from renewable resources. The industrial production of PHAs has already been used in practice by pure cultures. In recent years, many studies have been addressed of PHA production by mixed cultures. Nevertheless, while fermentation strategy to improve the PHA content of biomass, yield and productivity in pure cultures are well defined, knowledge about the operational condition for PHA synthesis by mixed culture is still very limited. The ecology of the microbial community of activated sludge remains largely unknown, primarily because of the difficulty of making detailed observation. Recently, developed molecular techniques allow determination of community composition from DNA extracted directly from biomass samples. This study examined the changes of bacterial communities in activated sludge through application of the molecular technique, ribosomal intergenic spacer analysis (RISA). Microbial communities from anaerobic-aerobic and ammonia limited fermentations were ascertained. The applied operational conditions were shown to select for a restricted microbial population, which were different in term of structure with respect to the initial microbial consortia in the activated sludge used as inoculum.