Louis-Félix Henneguy (18 March 1850 – 16 January 1928) was a French zoologist and embryologist born in Paris.
In 1875, he received his medical doctorate from the University of Montpellier with a dissertation on the physiological action of poisons, Étude physiologique sur l'action des poisons. In 1883 he obtained his agrégation with Les lichens utiles, a thesis on useful lichens.
During his career he was a professor of comparative embryology at the Collège de France (1900–28), and a member of the Académie de Médecine, the Académie d'Agriculture and the Académie des sciences (1908–28). From 1894 he was director of the journal, Archives d'anatomie microscopique.
He is known for his extensive research of phylloxera, publishing a number of papers on means of destroying its eggs during the winter (1885, 1887–88). Also he performed studies on the natural history of the apple blossom weevil, proposing methods for its eradication (1891). On behalf of the Marine Fisheries Advisory Committee, he did reviews involving the sale and consumption of mussels throughout the year.
With Hungarian neuroanatomist, Mihály Lenhossék (1863–1937), the "Henneguy–Lenhossek theory" is named, which states the claim that mitotic centrioles and ciliary basal kinetosomes are fundamentally the same structure.