VQ-domain proteins are known to interact with WRKY transcription factors and have been reported to be involved in plant defence responses to environmental stresses in Arabidopsis. Thus, elucidation of the defence mechanisms during the interaction of VQ-domain proteins and WRKY transcription factors could provide useful insights into the regulation of VQ-domain protein-mediated WRKY transcription factors. As the focus of this review, we summarize the genomic analysis of the VQ-domain proteins as one of the WRKY-interacting proteins and their biological effects during plant stress conditions in Arabidopsis and rice.