To screen antagonistic endophytic bacteria isolated from the plant of Anemarrhena asphodeloides, of which could inhibit six common diseases of Panax ginseng and three ones of Asarum sclerotium, to provide a base for biological control of some Chinese medicinal materials. The antagonistic endophytic bacteria were isolated and screened by tissue slicing, tissue grinding and hyphal growth rate. The strains with significant bacteriostatic activity（P＜0.05） were identified according to 16S rDNA sequence and phylogenetic tree analysis, and the bacteriostatic rate of fermentation broth of active strains was detected by hyphal growth rate method. The fermentation conditions of the strain were optimized by orthogonal test. From the 359 endophytic bacteria isolated from the plant of A. asphodeloides three endophytic bacteria were screened, they are strains of BR10, BR11 and BR26, and all of them have had antagonistic effect and strong bacteriostatic activities to the nine pathogens, there was a highest bacteriostatic rate 92.41% of them. The results of phylogenetic analysis of 16S rDNA sequence showed that the BR11 had the closest relationship with many strains of Rahnella aquatilis, and was in the same branch of the phylogenetic tree, so the BR11 strain was identified as R. aquatilis. The optimum medium formula and culture conditions of BR11 strains were determined: beef paste 1.5%, glucose 1.5%, yeast extract 0.5%, MgSO₄ 0.15%, initial pH value 7.5, temperature 29 ℃, fermentation time 72 h. The endophytic bacteria BR11 from A. asphodeloides is an excellent candidate for the control of ginseng and Asarum diseases.