This study investigated various groups of methanotrophic microorganisms, including the anaerobic methane-oxidizing archaea (ANME) group, aerobic methanotrophic bacteria, and bacteria of the phylum NC10 (Candidatus Methylomirabilis oxyfera). The polymerase chain reaction (PCR) technique was employed with specific primers for the pmoA gene from the aerobic methanotrophic and M. Oxyfera methanotrophic denitrifying (NC10 phylum) and for the anaerobic methanotrophic archaea 16S rRNA gene (ANME-1 and ANME-2). Sludge and sediment samples were analyzed from different sewage treatment systems installed at the Sanitation Research and Training Center (CePTS) at the Arrudas wastewater treatment plant (Arrudas WWTP), in Belo Horizonte, Brazil. ANME was shown to be present in sludges from the upflow anaerobic sludge blanket (UASB) reactor and activated sludge system, and in sediments from the polishing pond and wetlands. On the other hand, aerobic methanotrophic bacteria were detected only in the polishing pond samples, while no methanotrophic denitrifiers of the M. oxyfera genre were detected at all. Besides investigating and detecting different groups of methanotrophs in the treatment systems, the study provided support for another in which samples from the systems analyzed were selected for use as inoculum for methane anaerobic oxidation potential experiments and methanotrophic microorganism enrichment.