DNA methylation is a conserved epigenetic mark in plants and many animals. How parental alleles interact in progeny to influence the epigenome is poorly understood. We analyzed the DNA methylomes of Arabidopsis Col and C24 ecotypes, and their hybrid progeny. Hy- brids displayed nonadditive DNA methylation levels, termed meth- ylation interactions, throughout the genome. Approximately 2,500 methylation interactions occurred at regions where parental DNA methylation levels are similar, whereas almost 1,000 were at differ- entially methylated regions in parents. Methylation interactions were characterized by an abundance of 24-nt small interfering RNAs. Furthermore, dysfunction of the RNA-directed DNA methylation pathway abolished methylation interactions but did not affect the increased biomass observed in hybrid progeny. Methylation interac- tions correlated with altered genetic variation within the genome, suggesting that they may play a role in genome evolution. Whole genome bisulfite sequencing and small RNA sequencing of the wild type and nrpd1nrpe1 double mutant background of parent Col ,C24, the hybrid ColXC24 and C24XCol to explore the role of the RdDM pathway in DNA methylation interactions.