Johann Jakob Kaup (April 10, 1803 - July 4, 1873) was a German naturalist.

He was born at Darmstadt. After studying at Göttingen and Heidelberg he spent two years at Leiden, where his attention was specially devoted to the amphibians and fishes. He then returned to Darmstadt as an assistant in the grand ducal museum, of which in 1840 he became inspector. In 1829 he published Skizze zur Entwickelungsgeschichte der europäischen Thierwelt, in which he regarded the animal world as developed from lower to higher forms, from the amphibians through the birds to the beasts of prey; but subsequently he repudiated this work as a youthful indiscretion, and on the publication of Darwin's Origin of Species he declared himself against its doctrines. The extensive fossil deposits in the neighbourhood of Darmstadt gave him ample opportunities for palaeontological inquiries, and he gained considerable reputation by his Beiträge zur näheren Kenntniss der urweltlichen Säugethiere (1855-1862). He also wrote Classification der Säugethiere und Vögel (1844), and, with Heinrich Georg Bronn (1800-1862) of Heidelberg, Die Gavial-artigen Reste aus dem Lias (1842-1844). He died at Darmstadt.