DNA methylation is an epigenetic mark associated with transcriptional repression and essential for proper vertebrate development. Because of its association with human development and disease, DNA methylation has stayed in the research focus for almost half a century. However, it is only since very recently that we are able to generate genome-wide maps of this mark and gain insight into the many roles DNA methylation plays during the vertebrate life cycle. The recent adaptation of next-generation sequencing technologies to global DNA methylation profiling has spurred a flurry of studies conducted on various model systems. The recent publications of zebrafish base-pair resolution methylomes provided key advances in our understanding of how DNA methylation is remodeled during early vertebrate embryogenesis and highlighted important differences in developmental strategies between mammals and lower vertebrates. Here, we review our understanding of the role of DNA methylation during vertebrate development and discuss the insights obtained from almost a decade of methylome studies.