Indole glucosinolates are known to play essential and diverse roles in Arabidopsis immunity to pathogens. However, a complete understanding of the function of these compounds in plant immunity remains unclear. In this study, we investigated the transcriptome profile in loss-of-function mutant of MYB51, the key transcription factor that controls the biosynthesis of indole glucosinolates. Upon treatment with flg22 (a 22-amino acid peptide derived from bacterial flagellin), the genes that responded in a MYB51-dependent manner were analyzed. The results suggested that MYB51 was possibly implicated in most resistance processes, including pathogen recognition, signal transduction and PR protein activation. Of note, several genes in the ethylene pathway and the WRKY family, including WRKY33, were induced by flg22 in a MYB51-dependent manner. WRKY33 and ethylene were demonstrated to be crucial regulators in plant immunity defense and are functionally upstream of MYB51 during MAMP triggered immunity (MTI). This result suggested a "positive feedback loop" between MYB51 and its upstream regulators.