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Objective To investigate the influence of Panax ginseng continuous cropping on the carbon substrate metabolic activity of microbes in soils sampled from Dafang, Huangni, and Wulidi in Jilin Province, China. Methods Soil metabolisms of soil communities were characterized by community level physiological profiles using BIOLOGTM EcoPlate. Results Soils sampled from the three sites were analyzed and their metabolic activities were compared. Principal component analysis explored the significant variance in metabolic function of microbial communities in soils, though the Shannon index and the evenness index of them were similar. Futhermore, two principal components (PC1 and PC2), which contributed 67.83% and 10.78% of total variance, were extracted respectively. And also, substrates significantly correlated with PC1 and PC2 at the three sampling sites were identified. Conclusion Characteristic of soil is the primary factor influencing microbial communities, and P. ginseng continuous cropping has significant influence on microbial community. Though soil samples show similar microbial metabolic profiles, microbial communities in rhizosphere soil are changed obviously during the cultivation of P. ginseng, which would finally result in the unbalance of microbial community. Phytopathogens would gradually be the predominants in rhizosphere soil and make P. ginseng sick.