Abstract: In order to explore the operation status of biogas project,the physical and chemical properties of slurry and the difference of microbial community structure,we investigated and sampled the biogas plants of 9 livestock farms in Sichuan province and Chongqing.The prokaryotic community compositions were investigated using 16 S rRNA amplicon high-throughput sequencing technique.The results show that the biogas plants in Sichuan province and Chongqing mainly deal with aquaculture sewage,not for the purpose of biogas production.There are no significant differences in physicochemical parameters between pig and cattle farms,such as TN,TP,NH₄⁺ and COD_Cr.Among the 14 biogas samples,Firmicutes,Bacteroidetes,Proteobacteria,Synergistetes and Verrucomicrobia are the dominant microorganisms,the five major types of bacteria account for more than 84% of the total number of bacterial clones.Proteobacteria is relatively abundance ranging between 45.0% and 69.3%in the pig farm biogas plant,which is significantly higher than that in the cattle farm.The Firmicutes and Bacteroidetes in the slurry of cattle farm are dominant compositions,in which the average of relative abundances of the two bacteria is 58.4%.The biogas slurry is dominated by Methanomicrobia and Methanobacteria,and the abundance of Methanomicrobia is significantly different between the two types of farms.Methanosaeta as an absolute advantage bacteria in pig farm slurry,reaches 84.1%-94.4%,while Methanosarcina has very little abundance.The average relative abundance of Methanosaeta in cattle farm slurry is 45.1%,which is lower than that in pig farm.Methanobrevibacter has a low abundance in pig farm slurry,accounting for only 5.1% of the total number of clones.However,it is found that in a large number of slurry samples,wxh3 and bn3 accounts for 78.6% and 66.7% of the total archaea,respectively.Further analysis shows that the ratio of NH₄⁺/TP has significant correlation with the relative abundance of Firmicutes,Chaol and Shannon index.The principal coordinate analysis and cluster analysis of the bacterial community in slurry can accurately identify the pig and cattle farm plants whether good running or poor operating.These methods can provide reference for the evaluation of the treatment effect of livestock manure.