DNA methylation and histone modification exert epigenetic control over gene 
expression. CHG methylation by CHROMOMETHYLASE3 (CMT3) depends on histone H3K9 
dimethylation (H3K9me2), but the mechanism underlying this relationship is 
poorly understood. Here, we report multiple lines of evidence that CMT3 
interacts with H3K9me2-containing nucleosomes. CMT3 genome locations nearly 
perfectly correlated with H3K9me2, and CMT3 stably associated with 
H3K9me2-containing nucleosomes. Crystal structures of maize CMT3 homolog ZMET2, 
in complex with H3K9me2 peptides, showed that ZMET2 binds H3K9me2 via both bromo 
adjacent homology (BAH) and chromo domains. The structures reveal an aromatic 
cage within both BAH and chromo domains as interaction interfaces that capture 
H3K9me2. Mutations that abolish either interaction disrupt CMT3 binding to 
nucleosomes and show a complete loss of CMT3 activity in vivo. Our study 
establishes dual recognition of H3K9me2 marks by BAH and chromo domains and 
reveals a distinct mechanism of interplay between DNA methylation and histone 
modification.