[Objective] Unveil the characteristics of prokaryotic (bacteria and archaea) community structure of household biogas digesters in the tropical climate zones of Yunnan. [Methods] 16S rRNA gene clone library technique was constructed to study prokaryotic (bacteria and archaea) diversity of the household biogas digesters in Yunnan (north) typical tropical climate zones. [Results] Total 330 effective sequences of bacteria were obtained and divided into 108 OTUs, bacterial library coverage is 81.5%; 185 archaeal effective sequences were obtained and divided into 17 OTUs, archaeal library coverage is 97.8%. A typical sequence in each OTUs was selected and to perform similarity comparison and analysis in the GenBank database, the results showed that: most bacteria are uncultured bacteria (24.19%), the dominant bacterial phyla include Bacteroidetes (23.58%), Chloroflexi (21.46%), Firmicutes (13.91%) and Proteobacteria (8.74%); the dominant archaeal group is Methanosaeta (76.75%) of the order Methanosarcinales which is aceticlastic. In addition, a small amount of uncultured Crenarchaeota archaea (9.19%) was detected. [Conclusion] The results showed that microbial species are very rich in the household biogas digesters of Yunnan (north) typical tropical climate zones, different microbial species have obvious differences in the abundance and have obvious dominant population, and the diversity of bacteria is more abundant than that of archaea.