Abstract: This work is to screen and identify the endophytic bacteria from medicinal Isatis indigotica in the Hexi Corridor of Gansu Province against Fusarium moniliforme，Alternaria alternate，and Exserohilum turcicum. Endophytic bacteria were isolated from the roots，stems，leaves，petioles and flowers of I. indigotica using conventional separation method，from which the antagonistic bacteria were screened by the synchronous culture method，and the screened active endophytic bacteria were identified based on phenotypical and biochemical properties as well as its 16S rRNA gene sequence. As results，a total of 19 endophytes were isolated，and 10 strains of them had varied inhibition effects on F. moniliforme，accounting for the 52.6% of total isolates；the inhibition effect of strain G2 on F. moniliforme was the strongest with inhibition rates up to 94.63%. All 19 strains of the isolates had varied inhibition effects on A. alternata and E. turcicum，accounting for 100% of the total number of isolates. Among these strains，G2，J1，Y5 and B2 were selected for further study，and their inhibitory rates nearly reached 100%. Combined with the physiological and biochemical characteristics，colony characteristics，cell morphological characteristics and 16S rRNA sequencing results，the strains J1 and Y5 were identified as Microbacterium maritypicum，and the strain G2 and B2 as Kocuria rosea and Brachybacterium ginsengisoli，respectively. In summary，antagonistic bacteria on the plant pathogens were isolated from I. indigotica，especially the strain G2，J1，Y5 and B2 presented the strongest inhibitory effects，and thus their inhibitory activities will be worthwhile for further studies.

Key words: Isatis indigotica, endophytic bacteria, phytopathogen, antifungal activity, 16S rRNA