► I examine recent reports examining epigenetic variation in wild plant populations. ► DNA methylation polymorphism patterns in populations suggest adaptive variation. ► Disentangling genetic and epigenetic variation remains a significant challenge. ► Integration of molecular and population studies is needed to understand epigenetics. Researchers are beginning to use wild plant populations to survey and assess cytosine methylation polymorphisms in a population and ecological genetic framework. These studies support the plausibility of adaptive epigenetic alleles, but uncertainty remains due to the difficulty in untangling genetic and epigenetic variation in wild populations. The increasing emphasis on stress-induced epigenetic alterations and transgenerational phenomena among researchers focused on epigenetic mechanisms should push practitioners of this subfield to consider the questions and tools of colleagues grappling with epigenetics from ecological and evolutionary perspectives.