The potato industry relies on sprout inhibitors like 1,4-dimethylnaphthalene (DMN) to maintain tuber dormancy during storage. DMN’s mechanism of inhibiting sprout growth is currently unknown; this study considered the epigenetic mechanism of DNA methylation as a possible connection between DMN and the changes in gene expression observed in potatoes after DMN exposure. Methylation rate and sites were compared between treatment and control potatoes, and genes possibly under the control of promoter methylation were identified.