Early embryonic development occurs in the absence of transcription; instead, it relies on maternal mRNAs and proteins present within the egg. It is believed that this period of transcriptional quiescence is maintained by factors that eventually become titrated out during early cleavages, thus leading to zygotic genome activation. How exactly this transition occurs, however, is unclear. Here, Jim Smith, Steven Harvey and co-workers use exome sequencing and RNA-seq to distinguish between maternal and zygotic transcriptomes in early zebrafish embryos (p. 2703). Using single nucleotide polymorphisms to identify maternal and paternal transcriptomes, and using the appearance of paternal mRNAs as an indicator of zygotic transcription, the researchers identify the first zygotic genes to be expressed in the embryo. Zygotic transcription, they report, begins after ten cycles. Prior to this, changes in mRNA levels are observed but these are due to post-transcriptional regulation of maternal mRNAs and not due to transcription. Finally, the researchers demonstrate that different modes of regulation are required for zygotic transcription initiation.