Brian K. Hall writes in the Scientific American:
The study of embryonic stages across the animal kingdom–comparative embryology–flourished from 1830 on. Consequently, when On the Origin of Species appeared in 1859, Charles Darwin knew that the embryos of all invertebrates (worms, sea urchins, lobsters) and vertebrates (fish, serpents, birds, mammals) share embryonic stages so similar (which is to say, so conserved throughout evolution) that the same names can be given to equivalent stages in different organisms. Darwin also knew that early embryonic development is based on similar layers of cells and similar patterns of cell movement that generate the forms of embryos and of their organ systems. He embraced this community of embryonic development. Indeed, it could be argued that evo devo (then known as evolutionary embryology) was born when Darwin concluded that the study of embryos would provide the best evidence for evolution.
Darwin’s perception was given a theoretical basis and evo devo its first theory when Ernst Haeckel proposed that because ontogeny (development) recapitulates phylogeny (evolutionary history), evolution could be studied in embryos. Technological advances in histological sectioning and staining made simultaneously in the 1860s and 1870s enabled biologists to compare the embryos of different organisms. Though false in its strictest form, Haeckel’s theory lured most morphologists into abandoning the study of adult organisms in favor of embryos–literally to seek evolution in embryos. History does repeat itself; 100 years later a theory of how the body plan of a fruit fly is established, coupled with technological advances, ushered in the molecular phase of evo devo evaluated by Carroll.
Read more here.