BACKGROUNDPlant bacterial infections and plant viruses seriously affected the yield and quality of crops. Based on the variety activities of tryptanthrin, a series of tryptanthrin analogues bearing F and piperazine moieties were designed, synthesized, and evaluated for their biological activities against three plant bacteria and tobacco mosaic virus (TMV).RESULTSBioassay results indicated that compounds 6a‐6l displayed excellent antibacterial activities in vitro and 6a‐6c, 6g exhibited better antiviral activities against TMV than commercial ribavirin. Especially, 6b showed the most effect on Xanthomonas oryzae pv. Oryzae (Xoo) with the EC50 of 1.26 μg ml−1, compared with commercial pesticide Bismerthiazol (BT, EC50 = 34.3 μg ml−1) and Thiodiazole copper (TC, EC50 = 73.3 μg ml−1), respectively. Meanwhile, 6a also had the best antiviral activity at 500 μg ml−1 for curative, protection, and inactivation activities, compared with ribavirin in vivo.CONCLUSIONCompound 6b could cause changes in bacterial morphology, induce the accumulation of reactive oxygen species (ROS), promote apoptosis of bacterial cells, inhibit the formation of biofilm, and block the growth of Xoo cells. Proteomic analysis revealed major differences in the bacterial secretory system pathways T2SS and T6SS, which inhibited membrane transport. Molecular docking revealed 6a and 6g could interact with TMV coat protein preventing virus assembly. These results suggested tryptanthrin analogues bearing F and piperazine moieties could be agricultural drugs as promising candidate agents.This article is protected by copyright. All rights reserved.