Repetitive DNA sequences in the genome can cause problems for our cells. To protect the genome, cells turn off these repetitive sequences by placing them in inactive heterochromatic areas and adding repressive markers. However, we don’t know exactly how this is achieved during early embryonic development. Here, we found that the repetitive sequences are densely labeled with an active marker H3K14ac. This marker to our surprise attracts a protein called Eggless/SetDB1 to foster a repressive environment, turning off these repetitive sequences in early fruit fly embryos. Experimentally disrupting this process unleashes many repetitive DNA sequences and harms organismal viability. Our finding uncovers a mode to turn off repetitive sequences in the development of early embryos