Five types of sulfate-reducing passive bioreactors with rice bran as substrate were operated at three different mine sites under various operating conditions to investigate and compare the dominant sulfate-reducing bacteria (SRBs) involved in acid mine drainage (AMD) treatment. In all bioreactors, AMD was properly treated under the national effluent standard of Japan when 16 samples in total were taken from different depths of the bioreactors at different sampling times. Analysis of the microbiomes in the five bioreactors by Illumina sequencing showed that Desulfosporosinus spp. were dominant SRBs in all bioreactors (the relative abundances were similar to 26.0% of the total population) regardless of reactor configurations, sizes, and operating conditions. This genus is known to comprise spore-forming, acid-tolerant, and oxygen-resistant SRBs with versatile metabolic capabilities. Microbial populations of AMD water and soil samples (as inocula) from the respective mine sites were also analyzed to investigate the origin of the genus Desulfosporosinus. Desulfosporosinus spp. were detectable in most AMD water samples, even at low relative abundances (0.0025 to 0.0069% of total AMD population), suggesting that the genus Desulfosporosinus is present within the AMD water that flows into the bioreactor. These data strongly imply that the passive treatment system is a versatile and widely applicable process for AMD treatment.