Display omitted •Petroleum refinery wastewater is poorly treated in CSTR.•Higher performance treatment was achieved in MBR inoculated with the same consortium than CSTR.•Biomass concentration increased rapidly in MBR but declined in the CSTR due to high toxicity.•The MBR presented a higher bacterial abundance and diversity than the CSTR.•Identification of major acclimated bacterial genera in the MBR could explain its high performance treatment. This study evaluated firstly the performance of the Continuous Stirred Tank bioReactor system (CSTR) for the treatment of highly toxic petroleum refinery wastewaters at the pilot-scale. The reduction of the COD, BOD5, phenols, and the total petroleum hydrocarbon (TPH) reached 82.10%, 85.87%, 91.63%, and 81.11%, respectively at high hydraulic residence time (HRT = 10 days). Decreasing HRT to 5 and 2.5 days led to a decrease in the efficiency of the process and a decrease in biomass concentration was also observed (<1000 mg/l). We investigated to test Membrane Bioreactor (MBR) configuration inoculated with the same microbial consortium of CSTR. Therefore, the removal efficiency reached 89.14% of COD and biomass concentration increased to 2800 mg/l at HRT = 1 day. Microbial biomass showed high acclimatization to the toxic wastewater. Communities’ abundance and composition in CSTR and MBR were then performed using culture-independents approaches (qPCR, Illumina Miseq sequencing, and DGGE) based on the 16S rRNA gene sequencing. Results showed that major genera affiliated with Betaproteobacteria and Gammaproteobacteria were commonly shared in both bioreactors. The MBR presented a higher bacterial abundance and diversity than the CSTR. Furthermore, dominant genera belonging to Alphaproteobacteria and Bacteroidetes were exclusively detected in CSTR and MBR, respectively. Six potential hydrocabonclastic bacteria were isolated from the CSTR. This study demonstrates the occurrence of specific acclimated bacterial communities in MBR different from those identified in CSTR, improving the petroleum hydrocarbon wastewater treatment. The results would be useful in developing an MBR system for treating toxic stripped wastewater at a larger scale.