The relationship between embryonic development and evolution historically investigated based on embryo morphology could now be reassessed using mRNA expression endophenotype. Here, we analyzed the conservation of divergence of the developmental mRNA expression profiles in nine evolutionarily distinct species, from oyster to mouse, and compared them to the original concepts formulated by von Baer and Haeckel. We find nearly linear conservation of species’ developmental programs among these species, compatible with models rooted on von Baer’s postulates, for approximately a third of expressed orthologous genes. By contrast, 5-15% of developmental expression profiles, enriched in neural genes, displayed an alignment pattern compatible with the terminal edition paradigm proposed by Haeckel. Thus, the development-evolution relationship based on mRNA expression agrees with early concepts based on embryo morphology and demonstrates that the corresponding patterns coexist in chordate development.