Cytosine DNA methylation is a mechanism of epigenetic inheritance widespread among eukaryotes, including plants and animals. DNA methylation has been recruited by evolution for multiple functions, including transposon silencing and gene regulation, which are carried out by influencing nucleosome composition and placement, among other mechanisms. Proper methylation patterns are essential for mammalian and plant development and are disrupted in cancer. Despite their importance, DNA methylation systems vary considerably among eukaryotes, revealing a rich and complex evolutionary history that can elucidate mechanistic and functional studies. I will discuss my laboratory’s work to understand DNA methylation evolution, mechanism of inheritance, function, and influence on genome sequence composition and gene structure.