Abstract: Stem cells are a group of pluripotent cells that can differentiate into a diverse range of specialized cell types. They continuously provide new cells for organogenesis, wound repair, and regeneration in multicellular organisms. Stem cell specification and differentiation are orchestrated by complex gene regulatory networks. In addition, epigenetic regulation plays a crucial role in many biological events, including stem cell determination. In this review, we summarize recent advances in epigenetic control of root stem cells in the model plant Arabidopsis thaliana. Specifically, we focus on the interplay between epigenetic regulators and stem cell-controlling key transcription factors, which regulates root stem cell self-renewal and differentiation in plants.