This study focused on comparing bacterial communities from two lab-scale sequencing batch reactors (SBR) operated in nitritation and nitratation mode, respectively. Four samples were collected until the bioreactors had been run at a stable and efficient nitrogen conversion at different operational temperatures of 22 degrees C and 12 degrees C. The bacterial community compositions were profiled by Illumina MiSeq sequencing and quantitative real-time (q-PCR). Sequencing results indicated that bacterial compositions in the two reactors at the phylum level showed a similar structure with the decreased temperature, while the disparity between respective heterotrophic communities was clearly demonstrated at the genus level except autotrophic nitrogen-oxidizing species, Nitrosomonas and Nitrobacter highly enriched inside the bioreactors. In addition, the dominated Nitrosomonas and Nitrobacter were further checked through q-PCR and high concentration heterotrophic denitrifiers using nirK as gene markers were also found, consistent with a variety of potential heterotrophs analyzed by high-throughput sequencing. Due to the weak effect of temperature on bacterial communities of different functional nitrifying sludge, heterotrophic communities possibly depended on the influent substrate. Taking into account these results, heterotrophic bacterial communities coexisting with ammonia-oxidizing bacteria (AOB) or nitrite-oxidizing bacteria (NOB) were mutually different and distinct in the diversity and stability.