The authors present a single-cell bisulfite sequencing method (scBS-Seq) that accurately measures DNA methylation at up to 48.4% of CpGs. This method is designed to overcome the limitations of traditional bisulfite sequencing by performing bisulfite conversion first, followed by DNA fragmentation and random priming. The technique was tested on metaphase-II oocytes and mouse embryonic stem cells (ESCs) cultured under different conditions, revealing epigenetic heterogeneity in both cell types. ScBS-Seq demonstrated high reproducibility and accuracy, with an average mapping efficiency of 24.6% and methylation scores on an average of 3.7 million CpG dinucleotides. The method was able to capture the entire DNA methylome of oocytes using only 12 single cells, and it revealed significant DNA methylation heterogeneity within ESCs, particularly in regions associated with active enhancers. ScBS-Seq provides a powerful tool for studying epigenetic heterogeneity in rare and heterogeneous cell populations, offering insights into gene regulation and early embryonic development.The authors present a single-cell bisulfite sequencing method (scBS-Seq) that accurately measures DNA methylation at up to 48.4% of CpGs. This method is designed to overcome the limitations of traditional bisulfite sequencing by performing bisulfite conversion first, followed by DNA fragmentation and random priming. The technique was tested on metaphase-II oocytes and mouse embryonic stem cells (ESCs) cultured under different conditions, revealing epigenetic heterogeneity in both cell types. ScBS-Seq demonstrated high reproducibility and accuracy, with an average mapping efficiency of 24.6% and methylation scores on an average of 3.7 million CpG dinucleotides. The method was able to capture the entire DNA methylome of oocytes using only 12 single cells, and it revealed significant DNA methylation heterogeneity within ESCs, particularly in regions associated with active enhancers. ScBS-Seq provides a powerful tool for studying epigenetic heterogeneity in rare and heterogeneous cell populations, offering insights into gene regulation and early embryonic development.