Malus domestica, or orchard apple, is clonally propagated to maintain ideal varieties. Unlike other species where plant breeding efforts have harnessed natural variation through genetic crosses, many fruits are the result of clonal propagation and are based on a single genetic variety. This method of vegetative propagation presents multiple opportunities for the generation, accumulation and leverage of epigenetic variation (Springer and Schmitz, 2017). Epialleles may arise through spontaneous, developmental or environmental mechanisms and could also be associated with genetic changes. On a single tree, morphological variants can arise, sometimes with new desirable characteristics, which are then captured through vegetative propagation to form new ‘sports’. However, sports are also prone to reversion, suggesting the possibility of epigenetic control. Spontaneous or induced epialleles may be stably maintained and propagated through grafting, although the accumulation rate and stability in clonal species such as apple is largely unknown. Grafting also presents an opportunity for directed epigenetic changes from the rootstock to scion or vice versa (Lewsey et al., 2016; Melnyk et al., 2011). Here we perform whole genome bisulfite sequencing on 19 samples from Honeycrisp and Minneiska apple trees. Together with data from Golden Delicious, we investigate associations between DNA methylation variation and 1) generation, 2) rootstock and 3) sports. The most pronounced variation observed is heterozygous loss of DNA methylation that is only seen in a single tree, suggesting widespread loss of DNA methylation for one allele but not the other. Heterozygous gains of methylation were less frequent. The analysis of multiple samples of the same tree from different branches reveals a number of shared heterozygous losses but also provides an estimate of the frequency of new losses based on differences accumulated within the same individual. These findings have implications for spontaneous variation and trait stability in breeding of clonal and long-lived species.