DNA methylation is a conserved and vital epigenetic modification that plays essential roles in plant growth, development, and responses to environmental stress. Cytosine-5 DNA methyltransferases (C5-MTases) and DNA demethylases (dMTases) are key regulators of DNA methylation dynamics. However, a comprehensive characterization of these gene families in sweet potato has remained elusive. In this study, we systematically identified and analyzed eight C5-MTase and five dMTase genes in the genomes of diploid (Ipomoea trifida, 2n = 2x = 30) and autohexaploid (Ipomoea batatas, 2n = 6x = 90) sweet potato. Phylogenetic, structural, and synteny analyses revealed a high degree of conservation among these genes, suggesting their essential roles during evolution. Promoter analysis uncovered multiple cis-acting elements, particularly those responsive to light and hormones. In addition, we examined the expression profiling of IbC5-MTases and IbdMTases genes during storage root development, revealing that several were highly expressed during the early and rapid expansion stages. These findings suggest that C5-MTases and dMTases may contribute to the regulation of storage root formation in sweet potato through epigenetic mechanisms, offering valuable insights for future functional studies and epigenetic breeding efforts.