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Heritable epigenetic polymorphisms, such as differential cytosine methylation, can underlie phenotypic variation^,. Moreover, wild strains of the plant Arabidopsis thaliana differ in many epialleles^,, and these can influence the expression of nearby genes^,. However, to understand their role in evolution, it is imperative to ascertain the emergence rate and stability of epialleles, including those that are not due to structural variation. We have compared genome-wide DNA methylation among 10 A. thaliana lines, derived 30 generations ago from a common ancestor. Epimutations at individual positions were easily detected, and close to 30,000 cytosines in each strain were differentially methylated. In contrast, larger regions of contiguous methylation were much more stable, and the frequency of changes was in the same low range as that of DNA mutations. Like individual positions, the same regions were often affected by …