Objective To group and characterize natural plague foci in China. Methods A novel two-class typing method as well as a three-indication nomenclature method were established to group and characterize the natural plague foci, on the basis of eco-geographical landscapes of plague foci, genetics of Yersinia pestis, zoology of rodent reservoirs and the entomology of flea vectors. Results A total of 12 distinct natural plague foci (including 19 subtypes) as well as their biological features were characterized. Conclusion Natural plague foci in China were grouped and characterized in this study.