A method of high-throughput sequencing of gene libraries was used to identify the microbial communities in samples of sewage sludge at waste treatment facilities in Saint Petersburg, Russia. It was established that the waste had a complicated taxonomic structure and consisted of two main domains: Archaea (8.4% average) and Bacteria (77.6% average). The Archaea domain included three phyla (methanogens): Euryarchaeota, Crenarchaeota and Parvarchaeota. The Bacteria domain was represented by 49 phyla, including Proteobacteria, Firmicutes, Bacteroidetes, Chloroflexi, Cyanobacteria, Planctomycetes, Gemmatimonadetes, Acidobacteria and Verrucomicrobia. Up to 2.8% share of methanogens in sewage sludge deposited in landfills for around 15 years indicated the ongoing destruction of organic matter. In addition, ten pathogenic microorganisms were detected, including Clostridium and Mycobacterium. The results indicated that the national regulatory requirements for waste in Russia need to be reviewed in terms of compiling a list of standardised indicators for environmental monitoring of landfill sites.