Heterochromatin is a key architectural feature of eukaryotic genomes, crucial for silencing of repetitive elements and maintaining genome stability. Heterochromatin shows stereotypical enrichment patterns around centromeres and repetitive sequences, but the molecular details of how heterochromatin is established in vivo are poorly understood. Here, we map the genome-wide distribution of H3K9me3-dependent heterochromatin in individual Drosophila early embryos at precisely staged developmental time points.