Gametogenesis is dependent on the expression of germline-specific genes. However, it remains unknown how the germline epigenome is distinctly established from that of somatic lineages. Here we show that genes commonly expressed in somatic lineages and spermatogenesis-progenitor cells undergo repression in a genome-wide manner in late stages of the male germline and identify underlying mechanisms. SCML2, a germline-specific subunit of a Polycomb repressive complex 1 (PRC1), establishes the unique epigenome of the male germline through two distinct antithetical mechanisms. SCML2 works with PRC1 and promotes RNF2-dependent ubiquitination of H2A, thereby marking somatic/progenitor genes on autosomes for repression. Paradoxically, SCML2 also prevents RNF2-dependent ubiquitination of H2A on sex chromosomes during meiosis, thereby enabling unique epigenetic programming of sex chromosomes for male reproduction. Our results reveal divergent mechanisms involving a shared regulator by which the male germline epigenome is distinguished from that of the soma and progenitor cells. Display omitted •SCML2 regulates global silencing of somatic/progenitor genes in the male germline•SCML2 is a germline-specific subunit of Polycomb repressive complex 1•SCML2 establishes H2A ubiquitination to silence somatic/progenitor genes on autosomes•SCML2 prevents H2A ubiquitination on meiotic sex chromosomes Hasegawa et al. show that SCML2, a germline-specific subunit of a Polycomb repressive complex 1, mediates genome-wide repression of genes commonly expressed in somatic lineages and spermatogenesis-progenitor cells in late stages of the male germline. SCML2 acts by differentially regulating histone H2A ubiquitination on autosomes versus meiotic sex chromosomes.