Abstract: Abstract: The microbial varieties of 5 biogas digesters (A08, A09, A010, A011, and A012) were investigated using high-throughput sequencing in different regions in Xinjiang. The operational taxonomic units (OTU) number of bacterial in the OTU cluster analysis of 5 biogas digesters was 2 105, and their identical OTU number was 225. The total OTU number of fungal was 2 224, and their identical OTU number was 178.The main types of biogas slurry samples, A08, A09, and A010, with cow manure as substrate were Bacteroidetes, Firmicutes, and Proteobacteria. The sample A011 with chicken manure as the substrate was mainly Bacteroides and Firmicutes, and the relative abundance was 58.5% and 23.8%, respectively. The sample A012 with pig manure as substrate was similar to the sample A09 with cow manure as substrate. The first dominant group was Firmicutes, the second dominant group was Bacteroides, and the third one was Proteobacteria. The main fungi in the 5 biogas slurry samples were Ascomycota and Basidiomycota at the phylum level, in which the relative abundance of Ascomycota accounted for the majority, reached 72.7%-83.3%, with a relatively abundant level of Basidiomycetes at 4.3%-7.3%. The Xinjiang biogas digesters contained an extremely abundant number of microbial strains, and the microbial distributions of the different samples were different, which provided theory evidence for the preparation of high efficiency biogas fermenting agents.