Objective To provide original reference data for oral ecosystem research, Tibet minipigs, beagle dogs, rhesus monkey, New Zealand white rabbits and Wistar rats were selected to study their respective characteristics of oral microbial mmunities and compared with normal data of humans. Methods Total DNA was extracted from the specimens of oral microbial communities of Tibet minipigs, beagle dogs, rhesus monkey, New Zealand white rabbits and Wistar rats, and used to amplify 16S rRNA V4 fragments with labeled universal primers. The diversity and structure of microbial communities from those animals were compared with that of humans using BIPES and QⅡME analysis after Illumina sequencing of 16S rRNA V4 fragments. Results The richness of the oral microbial communities of humans and the five species of laboratory animals was significantly different (P<0.05). Different species of animals have their own unique oral flora, among which the oral flora of the monkey is the most similar to that of humans. Conclusions Among the five species of laboratory animals, the oral microbial communities of rhesus monkeys and humans have highest similarity. Specifically, the Fusobacterium and Porphyromonas levels of rhesus monkeys is most similar to those of humans. Our findings indicate that rhesus monkeys may be suitable animal model for studies of human oral microbial communities. Tibet minipigs may be suitable animal model for Proteobacteria studies, while beagle dogs may be appropriate for modeling of diseases related to Spirochaetes.