The oocyte cytoplasm regulates and enhances the epigenetic asymmetry between parental genomes and, consequently, functional differences observed between them during development in mammals. Here we demonstrate a preferential interaction of HP1beta with the maternal genome immediately after fertilisation in the mouse zygote, which also shows a high level of lysine 9-methylated histone H3. In contrast, the paternal genome has neither HP1beta binding nor methylated histone H3 at these early stages. Paternal binding of HP1beta is only detected at the pronuclear stage, prior to the appearance of lysine 9-methylated histone H3. The early recruitment of heterochromatic factors specifically to the maternal genome could explain the preferential DNA demethylation of the paternal genome in the zygote.