Embryonic development involves the execution of the gene regulatory program driven by hierarchically organized transcription factor networks operating within the constraints of chromatin. Chromatin not only condenses and packages genomic DNA in the nucleus; it constitutes the key regulatory substrate for this gene regulatory program. Here we focus on the insights in chromatin dynamics obtained with Xenopus embryos and their conservation in other vertebrates. Major insights have been obtained by studies of histone variants, histone modifications, chromatin accessibility, and the interactions of chromatin with other factors during early development. We will discuss how histone modifications relate to chromatin assembly and the cell cycle and how they are influenced by DNA methylation. Changes in chromatin are at the basis of zygotic genome activation but also provide the molecular basis for developmental competence. This body of work illustrates how chromatin dynamics is regulated at many different levels and how this is tightly integrated with spatio-temporal programs of gene regulation.