Plants generate new organs through the activity of small populations of stem cells present in specialized niches called meristems. Stem cell homeostasis is attained by dynamic regulatory networks involving transcriptional regulators, hormones, and other intercellular signals that specify cell fate and convey positional information to the apical stem cells and the organizing center located immediately below. The balance between stem cell maintenance within the shoot apical meristem (SAM) and differentiation of cells that are displaced from the niche to form new organs involves the epigenetic silencing of stem cell regulatory genes. Recent advances have identified highly conserved chromatin remodeling factors as epigenetic regulators of stem cell fate that confer plasticity in plant development and ensure the stable inheritance of repressed expression states during organogenesis. These advances reveal that common mechanisms contribute to stem cell homeostasis in plants and animals.