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This work presented the sequences of activated sludge from two municipal wastewater treatment plants (WWTPs) located in a high altitude Plateau in Tibet, China (∼3650 m above the sea level). Sequencing data are the 16S rRNA gene amplicons of V4—V5 region that sequenced on an Illumina HiSeq PE250 platform. Data presented here include detail description and water quality parameters of the WWTPs as well as results of 16S rRNA gene sequences from their active sludges. The core microbial communities in the WWTPs were shown at the taxonomic level of phylum, class, order, family, genus and species. The sequencing data have been deposited in NCBI BioProject PRJNA477990 with the Biosample accessions SAMN09488330-SAMN09488338. The annotation of OTU table at the genus level was assessable on Zenodo ( https://zenodo.org/record/2105899#.XA0vQPZuJyw ).