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Summary Histone H3 lysine 9 (H3K9) methylation is unevenly distributed in mammalian chromosomes. However, the molecular mechanism controlling the uneven distribution and its biological significance remain to be elucidated. Here, we show that JMJD1A and JMJD1B preferentially target H3K9 demethylation of gene-dense regions of chromosomes, thereby establishing an H3K9 hypomethylation state in euchromatin. JMJD1A/JMJD1B-deficient embryos died soon after implantation accompanying epiblast cell death. Furthermore, combined loss of JMJD1A and JMJD1B caused perturbed expression of metabolic genes and rapid cell death in embryonic stem cells (ESCs). These results indicate that JMJD1A/JMJD1B-meditated H3K9 demethylation has critical roles for early embryogenesis and ESC maintenance. Finally, genetic rescue experiments clarified that H3K9 overmethylation by G9A was the cause of the cell death and perturbed gene expression of JMJD1A/JMJD1B-depleted ESCs. We summarized that JMJD1A and JMJD1B, in combination, ensure early embryogenesis and ESC viability by establishing the correct H3K9 methylated epigenome., Highlights • JMJD1A/JMJD1B have redundant but essential roles for ESC survival • JMJD1A/JMJD1B target H3K9 demethylation at gene-dense euchromatin • JMJD1A/JMJD1B and G9A play collaborative roles in tuning H3K9me2 levels, Kuroki et al. showed that H3K9 demethylases JMJD1A and JMJD1B are redundantly but essentially required for ESC survival and early embryogenesis in mice. JMJD1A and JMJD1B ensure transcription accuracy by demethylating H3K9 at gene-dense euchromatin.