The dynamics of gene expression in vertebrate embryogenesis at single cell resolution Time series of single cell transcriptome measurements can help us reconstruct the dynamics of cell differentiation in both embryonic and adult tissues. We produced such a time series of single cell transcriptomes from whole frog embryos, spanning zygotic genome activation through early organogenesis. From the data we derive a detailed catalog of cell states in vertebrate development, and show that these states can be assembled into temporal maps tracking cells as they differentiate over time. The inferred developmental transitions recapitulate known lineage relationships, and associate new regulators and marker genes with each lineage. We find that many embryonic cell states appear far earlier than previously appreciated, and assess conflicting models of vertebrate neural crest development. By further incorporating a matched time series of zebrafish from a companion paper, we perform global analyses across lineages, time, and species, revealing similarities and differences in developmental gene expression programs between frog and fish.