A bench-scale bioreactor was operated under two different technologies of membrane bioreactor and hybrid moving bed bioreactor-membrane bioreactor at hydraulic retention time 6-16h, sludge retention time 6-24 days, and mixed liquor suspended solids 3400-7800mgL(-1). Analyses of their bacterial community structures showed marked differences between the two technologies for global communities but not for dominant phylotypes, and the domination of different bacterial phylotypes for the different operational conditions. Tetrasphaera genus was ubiquitous (1.1%-19.2% relative abundance) in both bioprocesses. Fodinibacter (0.04%-7.75%) was found to positively correlate with other dominant phylotypes, highlighting the relevance of Intrasporangiaceae family in membrane-based technologies. Oligotypes distribution of dominant phylotypes showed that certain strains were favored at all operational conditions. Linkage with operational conditions determined that the presence/absence of carriers deeply impacted the relative abundance of dominant phylotypes. The results are relevant to discern the effect of operational conditions over bacterial communities in membrane-based technologies. (c) 2018 American Institute of Chemical Engineers AIChE J, 65: 536-548, 2019