This chapter reviews the epigenetic control of transposable elements (TEs) and their roles in various biological processes. We first demonstrated how epigenetic modifications influence the transposition activity and transcriptional expression of transposons, focusing on key regulatory mechanisms such as DNA methylation and histone modifications—including methylation, demethylation, and acetylation—and their effects on transposon silencing and activation. We then describe the contributions of transposons and transposon-derived genes to genome architecture and epigenetic regulation, including their roles in genome size evolution, chromatin accessibility, DNA and histone methylation/demethylation, histone acetylation/deacetylation, and the regulation of noncoding RNA (ncRNA) expression. Finally, we highlight the significance of epigenetic regulation of TEs in embryonic development, cellular reprogramming, tumorigenesis, and age-related diseases, underscoring the central role of coordinated epigenetic control of transposons in determining cell fate and disease outcomes.