Objective: To explore the epidemic situation of animal plague in Junggar Basin natural plague foci. Methods: Data on epidemics of plague and on population involved, as well as results on antibodies and pathogens, were analyzed. Samples on animals and vectors were collected from 18 counties in Junggar Basin plague natural foci between 2007 and 2016. Results: The density of Rhombomys (R.) opimus was temporally fluctuant, from 2.1/hm(2) to 22.6/hm(2) respectively. However, the spatial distribution appeared asymmetrical, with the highest seen in Kelamayi and Wumuqi-midong counties, as 14.2/hm(2) and 13.0/hm(2) respectively. Rates of capture on nocturnal rodents were from 4.2% to 10.1%, with the highest rate as 10.1% in 2014. Meriones meridianus appeared the dominant species in the nocturnal community of rodents, which accounted for 81.9%. Regarding the spatial and temporal distributions, rates of R. opimus with fleas appeared fluctuant, with an average rate as 90.7% and the average total flea index was 10.44. In flea community of R. opimus, Xenopsylla (X.) skrjabini was found the dominant species, popular in distribution and accounted for 47.8%. The average rate of nocturnal rodents with flea was 20.2%, with total flea index as 1.20 and the dominant fleas were X. conformis conformis and Nosopsyllus laeviceps. A total of 13 species with 9 087 serum samples from rodents were detected as having Y. pestis antibody by IHA, with 617 positive samples. Of them, the positive rate of having R. opimus appeared the highest (9.4%), followed by D. sagitta (1.1%). Spatially, two clustered areas were found, with one in the eastern Junggar Basin from Changji to Mulei county, with the antibody positive rates of R. opimus as 14.3%. The other one was in the central area of Junggar Basin, including Kelamayi, Shawan and Wusu counties, with the antibody positive rate as 13.6%. The prevalence of plague on R. opimus was fluctuant, with the lowest seen in 2008, with the average antibody positive rate of R. opimus as 1.0% and the highest as 19.3% in 2013. A total of 18 strains were isolated from 2007 to 2016. However, most of the strains were isolated from R. opimus and parasitic fleas, accounted for 8/9, in Kelamayi, Wulumuqi-midong and Jimusaer, respectively. Conclusions: Complex ecosystem was seen in the Junggar Basin natural plague foci, with the multiple composition of species and different community structure of hosts and vectors, plus the flustering prevalence. Animal plague was seen in the whole region with succession of the plague nature foci. Passive transmission of plague between human beings and animals through close contacts was seen which was driven by economic benefits to some degree.