DNA methylation is a key regulator of embryonic stem cell (ESC) biology, dynamically changing between naïve, primed, and differentiated states. The p53 tumor suppressor is a pivotal guardian of genomic stability, but its contributions to epigenetic regulation and stem cell biology are less explored. We report that, in naïve mouse ESCs (mESCs), p53 restricts the expression of the de novo DNA methyltransferases Dnmt3a and Dnmt3b while upregulating Tet1 and Tet2, which promote DNA demethylation. The DNA methylation imbalance in p53-deficient (p53 −/− ) mESCs is the result of augmented overall DNA methylation as well as increased methylation landscape heterogeneity. In differentiating p53−/− mESCs, elevated methylation persists, albeit more mildly. Importantly, concomitant with DNA methylation heterogeneity, p53−/− mESCs display increased cellular heterogeneity both in the "naïve" state and upon induced differentiation. This impact of p53 loss on 5-methylcytosine (5mC) heterogeneity was also evident in human ESCs and mouse embryos in vivo. Hence, p53 helps maintain DNA methylation homeostasis and clonal homogeneity, a function that may contribute to its tumor suppressor activity.[Keywords: DNA methylation; p53; stem cells] Supplemental material is available for this article. DNA methylation is a key epigenetic mark that is correlated with the major transitions during embryogenesis and other developmental processes. Differentiation and dedifferentiation of mouse embryonic stem cells (mESCs) provide a model for analyzing the regulation and possible functional roles of DNA methylation in maintaining pluripotency and facilitating differentiation. For example, when mESCs are induced to undergo differentiation, the transcriptional network ensuring pluripotency is silenced, and de novo DNA methylation is observed at promoters of key pluripotency factors (Thiagarajan et al. 2014). Conversely, when serum-maintained mESCs are moved to serum-free conditions with two kinase inhibitors (2i), their developmental potential is enhanced alongside substantial loss of DNA methylation . These transitions recapitulate early embryonic stages (Nichols and Smith 2009;Martin Gonzalez et al. 2016), but the mechanisms modulating DNA methylation remain to be fully characterized. The DNA methylation machinery is crucial for lineage specification, and mice lacking functional DNA methyltransferases (DNMTs) fail to develop properly (Siegfried and Cedar 1997;Smith and Meissner 2013); therefore, more comprehensive elucidation of the regulation of DNA methylation is pivotal to understanding the pluripotent state.In mammals, DNA methylation is governed by three DNMTs: Dnmt3a and Dnmt3b, responsible for setting de novo DNA methylation patterns, and Dnmt1, required primarily for maintenance of such patterns. In addition, TET enzymes (Tet1 and Tet2 in mESCs) facilitate demethylation by catalyzing oxidation of 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), which, by sequential oxidation steps, provides the substrate for reversal to unmethylated...