Although a few meiotically heritable epigenetic alleles have been identified in plants, not much is known about how they arise in populations. Joseph Ecker and colleagues now report the identification of spontaneously occurring DNA methylation epialleles in Arabidopsis thaliana mutation accumulation lines (Science, published online 15 September 2011; doi:10.1126/science.1212959). The authors generated base-resolution whole-genome methylation profiles of three ancestral and five descendant mutation accumulation lines. The genomes of all eight lines have been sequenced, allowing the authors to control for genetic variation. The majority of CGs were methylated in all eight lines. Analysis of sites of variable methylation showed that ancestral lines are highly similar when considered in terms of both CG single-methylation polymorphisms and differentially methylated regions. The authors identified 72 epialleles that contain methylation variation in the context of CG, CHG and CHH sequences and determined that these epialleles are not associated with genetic variation. They looked at eight epialleles that overlapped with protein-coding regions and found an association between mRNA expression levels and gain or loss of methylation at four of these loci. This work suggests that transgenerational epigenetic variation may account for more phenotypic diversity than was previously appreciated.