Emil Selenka (27 February, 1842, Braunschweig – 20 February, 1902, Munich) was a German zoologist. He is known for his research on invertebrates and apes and the scientific expeditions he organized to Southeast Asia and South America.
Selenka was the son of bookbinder Johannes Selenka (1801–1871). He studied natural history at the University of Göttingen, and following a graduate dissertation on Holothuroidea, he remained in Göttingen as an assistant to Wilhelm Moritz Keferstein (1833-1870). His research was in this period mainly on the anatomy, taxonomy and embryology of marine invertebrates, especially organisms from the phylum Echinodermata. In 1868 he became a professor of zoology and comparative anatomy at the University of Leiden, followed by a professorship at the University of Erlangen in 1874. In 1895 he was given an honorary professorship at the University of Munich. He was co-founder of the journal Biologisches Zentralblatt.
His later research was on mammals. He studied the early development of the embryo and the development of the germ layer in mammals, and did comparative anatomic research on apes, especially gibbons and orangutans. He found evidence that the lateral distribution of orangutan races was caused by geographic isolation (a process called allopatric speciation). Selenka also examined the evolution of marsupials and their morphologic relation with reptiles. One problem he was intereted in, was the evolutionary relation between Australian and South American marsupials.