A fundamental question in developmental biology relates to the connection between morphological stages and their underlying molecular activity. Here we demonstrate that, at the molecular level, embryonic development in five Caenorhabditis species proceeds through two distinct milestones in which the transcriptome is resistant to differences in species-specific developmental timings. By comparing the complete protein-coding transcriptomes of individually timed embryos across ten morphological markers, we found that developmental milestones can be characterized by their expression dynamics and activation of key developmental regulators. This approach led us to discover the nematode phylotypic stage and to show that in chordates and arthropods it is represented as two distinct stages, suggesting that animal body plans might evolve by uncoupling and elaboration on formerly synchronous processes.