DNA methylation is a cryptic phenomenon that invokes the methylation of the cytosines in nuclear DNA and is responsible for a wide variety of essential processes, starting from cellular differentiation (embryogenesis), transposon silencing, miRNA dependent methylation and gene regulation. This book presents an overview of different aspects of DNA methylation with a focus on its basic principles and mechanisms and gene silencing. Also discussed, is the role of DNA methylation in plants; epigenetic control of circadian clock operation; photoperiodic flowering; and DNA methylation in cancer and its role in multiple sclerosis.