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Summary Chromatin modifying activities inherent to polycomb repressive complexes PRC1 and PRC2 play an essential role in gene regulation, cellular differentiation, and development. However, the mechanisms by which these complexes recognize their target sites and function together to form repressive chromatin domains remain poorly understood. Recruitment of PRC1 to target sites has been proposed to occur through a hierarchical process, dependent on prior nucleation of PRC2 and placement of H3K27me3. Here, using a de novo targeting assay in mouse embryonic stem cells we unexpectedly discover that PRC1-dependent H2AK119ub1 leads to recruitment of PRC2 and H3K27me3 to effectively initiate a polycomb domain. This activity is restricted to variant PRC1 complexes, and genetic ablation experiments reveal that targeting of the variant PCGF1/PRC1 complex by KDM2B to CpG islands is required for normal polycomb domain formation and mouse development. These observations provide a surprising PRC1-dependent logic for PRC2 occupancy at target sites in vivo., Graphical Abstract, Highlights • Variant PRC1 complex-dependent H2AK119ub1 leads to binding of PRC2 and H3K27me3 • Canonical PRC1 complexes fail to efficiently deposit H2AK119ub1 and recruit PRC2 • A variant KDM2B/PCGF1/PRC1 complex is required for polycomb domain formation at CGIs • Failure to target KDM2B/PCGF1/PRC1 causes polycomb phenotypes and lethality in mice, Formation of repressive polycomb domains depends on histone ubiquitination catalyzed by variant PRC1 complexes at unmethylated CpG islands followed by PRC2 recruitment and methylation, rather than exclusively through initial association of PRC2.