In 1893, Julia Barlow Platt published her research on the origins of cartilage in the developing head of the common mudpuppy (Necturus maculosus) embryo. The mudpuppy is an aquatic salamander commonly used by embryologists because its large embryonic cells and nuclei are easy to see. Platt followed the paths of cells in developing mudpuppy embryos to see how embryonic cells migrated during the formation of the head. With her research, Platt challenged then current theories about germ layers, the types of cells in an early embryo that develop into adult cells. In most organisms' development, three types of germ layers are responsible for the formation of tissues and organs. The outermost layer is called ectoderm, the middle layer mesoderm, and the innermost layer endoderm, although Platt called it entoderm. Platt's research provided a basis for scientists to clarify the destination or function of the germ layers in vertebrates' development.

Ontogeny and Phylogeny is a book published in 1977, in which the author Stephen J. Gould, who worked in the US, tells a history of the theory of recapitulation. A theory of recapitulation aims to explain the relationship between the embryonic development of an organism (ontogeny) and the evolution of that organism's species (phylogeny). Although there are several variations of recapitulationist theories, most claim that during embryonic development an organism repeats the adult stages of organisms from those species in it's evolutionary history. Gould suggests that, although fewer biologists invoked recapitulation theories in the twentieth century compared to those in the nineteenth and eighteenth centuries, some aspects of the theory of recapitulation remained important for understanding evolution. Gould notes that the concepts of acceleration and retardation during development entail that changes in developmental timing (heterochrony) can result in a trait appearing either earlier or later than normal in developmental processes. Gould argues that these changes in the timing of embryonic development provide the raw materials or novelties upon which natural selection acts.

At the turn of the twentieth century, Edmund B. Wilson
performed experiments to show where germinal
matter was located in molluscs. At Columbia University in New York City,
New York, Wilson studied what causes cells to differentiate during
development. In 1904 he conducted his experiments on molluscs, and he modified the
theory about the location of germinal matter in the succeeding years. Wilson and others modified the
theory of germinal localization to accommodate results that showed
the significance of chromosomes in development and heredity.

The Stazione Zoologica Anton Dohrn (Anton Dohrn Zoological Station) is a public research institute focusing on biology and biodiversity. Hereafter called the Station, it was founded in Naples, Italy, in 1872 by Anton Dohrn. The type of research conducted at the Station has varied since it was created, though initial research focused on embryology. At the turn of the twentieth century, researchers at the Station established the sea urchin (Echinoidea) as a model organism for embryological research. A number of scientists conducted experiments on embryos and embryonic development at the Station from the 1890s to the 1930s, including Hans Driesch, Jacques Loeb, Theodor Boveri, Otto Warburg, Hans Spemann and Thomas Morgan. Research completed during this time at the Station contributed to the study of experimental embryology and developmental biology and helped shape the history of embryology.

Mutual Affinities of Organic Beings: Morphology: Embryology: Rudimentary Organs is the thirteenth chapter of Charles Darwin's book The Origin of Species, first published in England in 1859. The book details part of Darwin's argument for the common ancestry of life and natural selection as the cause of speciation. In this chapter, Darwin summarizes the evidence for evolution by connecting observations of development in organisms to the processes of natural selection. Darwin shows how the theory of special creation, which claims that God directly created all organisms in their current form, is inferior to the theory of natural selection for its ability to explain the diversity of life. In this chapter, Darwin also discusses classification and homology as they relate to natural selection.