This study investigates the microbial community and structure in the internal circulation (IC) reactors that treat wastewater from bagasse spraying, with (reactor B) and without (reactor A) addition of molasses alcohol wastewater (MAW). The V3 regions in the 16S rRNA of bacteria were sequenced using illumina sequencing to characterize the microbial community structures. The results showed that there were approximately 34.8% more microorganisms were reduced, while the proportions of the three most predominant bacterial populations especially some sulfate-reducing bacteria increased in reactor B. The archaeal community composition was measured by PCR-DGGE (denaturing gradient gel electrophoresis) analysis and sequencing some clones from the 16S rRNA gene library. The results showed that numerous, mostly uncharacterized, archaeal genera are present in reactors A and B; the genus Methanomethylovorans was only detected in the samples that received MAW. This study demonstrated the significant effect of MAW on microbial communities in the wastewater treatment bioreactor. (C) 2013 Elsevier Ltd. All rights reserved.