Abstract: To screen the tobacco endogenous genes responsive to multiple virus resistance (MVR), a mixture of 3 viruses (CMV, TMV, and PVY) was inoculated to Zhongyan100 and transgenic Zhongyan100. The samples of tobacco leaves were separately collected 6 hours and 3 weeks (when transgenic plant showed obvious character of MVR) after inoculation for transcriptome sequencing and qPCR analysis. Forty differential genes were obtained by further bioinformatics analysis, and out of them, 9 genes (enzymes and functional proteins) of obvious differential were identified through real-time qPCR.