SummaryWe have demonstrated that the Arabidopsis basic helix–loop–helix (bHLH) transcription factor, ABA‐responsive kinase substrate 1 (AKS1; also known as FLOWERING BHLH 3, FBH3), enhances K+ channel expression in guard cells leading to stomatal opening. The expression is suppressed by ABA‐induced phosphorylation of AKS1. Here we show that the phosphorylation results in the monomerization of AKS1 multimers and inhibits AKS1 binding to DNA. AKS1 forms homo‐multimers which dissociate following phosphorylation. Replacement of a critical amino acid in the bHLH domain inhibited multimer formation and decreased the binding of AKS1 to DNA. The monomerization was elicited via phosphorylation at three serine residues, which is mediated by SNF1‐related protein kinase 2.6 (SnRK2.6), in the vicinity of bHLH domain. Furthermore, ABA induced the phosphorylation‐dependent release of AKS1 from DNA, thereby suppressing transcriptional activity in vivo. Our results document a mechanism that inhibits gene expression by phosphorylation of a bHLH transcription factor.