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Numerous studies are investigating the basis of complex traits in a wide range of species (1). However, largely absent are efforts aimed at examining the possible contribution of natural epigenetic variation to heritable phenotypic diversity. Epigenetics is the study of heritable phenotypic variation that is not due to changes in the DNA sequence. Epigenetic variation is often overlooked because most populations used to analyze the basis of complex traits contain abundant DNA sequence variation—the major driver of phenotypic variation—and disentangling epigenetic variants from these sequence variants is a challenging task (2). On page 1145 of this issue, Cortijo et al. (3) demonstrate that epialleles (epigenetic alleles; alleles with the same DNA sequence but different DNA methylation patterns) are associated with heritable variation for two complex traits in the plant Arabidopsis thaliana. These results provide strong evidence that epialleles contribute to the heritability of complex traits and therefore provide a substrate on which Darwinian evolution may act.