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Background: The Junggar Basin plague focus was the most recently identified natural plague focus in China. Through extensive field investigations, great gerbils (Rhombomys opimus) have been confirmed as the main host in this focus, and the community structure of their parasitic fleas is associated with the intensity of plague epizootics. The aim of this study is to provide an indicator that can be surveyed to evaluate the risk of plague epizootics. Methods: Between 2005 and 2016, rodents and fleas were collected in the Junggar Basin plague focus. The parasitic fleas on great gerbils were harvested, and anti-F1 antibody in the serum or heart infusion of great gerbils was detected through indirect hemagglutination assay. Yersinia pestis (Y. pestis) was isolated from the liver and spleen of great gerbils and their parasitic fleas using Luria-Bertani plates. Receiver-operating characteristic (ROC) curve was used to evaluate the predictive value of flea index. Results: Between 2005 and 2016, 98 investigations were performed, and 6778 great gerbils and 68,498 fleas were collected. Twenty-seven rodents were positive for Y. pestis isolation with a positivity rate of 0.4%; 674 rodents were positive for anti-F1 antibody with a positivity rate of 9.9%. Among these 98 investigations, plague epizootics were confirmed in 13 instances by Y. pestis-positive rodents and in 59 instances by anti-F1 antibody-positive rodents. We observed a higher flea index among rodents with confirmed plague epizootic compared to the negative ones (P = 0.001, 0.002), with an AUC value of 0.659 (95% CI: 0.524–0.835, P = 0.038) for Y. pestis-positive rodents and an AUC value of 0.718 (95% CI: 0.687–0.784, P < 0.001) for anti-F1 antibody-positive rodents. Conclusions: Significantly higher flea index was associated with confirmed plague epizootic cases among great gerbils and could be used to predict plague epizootics in this focus. [ABSTRACT FROM AUTHOR]