Pharyngeal slits are filter-feeding organs found in Invertebrate chordates (lancelets and tunicates) and hemichordates living in aquatic environments. These repeated segments are controlled by similar developmental mechanisms. Some hemichordate species can have as many as 200 gill slits.Pharyngeal slits resembling gill slits are transiently present during the embryonic stages of tetrapod development. The presence of gill-like slits in the neck of the developing human embryo famously led Ernst Haeckel to postulate that "ontogeny recapitulates phylogeny"; this hypothesis, while false, contains elements of truth, as explored by Stephen Jay Gould in Ontogeny and Phylogeny. However, it is now accepted that it is the vertebrate pharyngeal pouches and not the neck slits that are homologous to the pharyngeal slits of invertebrate chordates. Gill slits are, at some stage of life, found in all chordates.
In vertebrates, the pharyngeal arches are derived from all three germ layers.Neural crest cells enter these arches where they contribute to craniofacial features such as bone and cartilage. However, the existence of pharyngeal structures before neural crest cells evolved is indicated by the existence of neural crest-independent mechanisms of pharyngeal arch development. The first, most anterior pharyngeal arch gives rise to the oral jaw. The second arch becomes the hyoid and jaw support. In fish, the other posterior arches contribute to the brachial skeleton, which support the gills; in tetrapods the anterior arches develop into components of the ear, tonsils, and thymus. The genetic and developmental basis of pharyngeal arch development is well characterized. It has been shown that Hox genes and other developmental genes such as dlx are important for patterning the anterior/posterior and dorsal/ventral axes of the branchial arches. Some fish species have jaws in their throat, known as pharyngeal jaws, which develop using the same genetic pathways involved in oral jaw formation.