Rathke was born in Christiania (now Oslo), Norway. He was the son of Casper Elias Rathke (1729-1777) and Margaretha Madsdatter Schultz (1735-1812). He was a student at the Christiania Cathedral School until 1787. Rathke took Cand.theol. at the University of Copenhagen in 1792, but soon left theology and began to study natural sciences.
In 1810, he became a professor at Copenhagen, where he also undertook lessons in botany and mineralogy beside zoology. In 1813, he moved to the University of Christiania (now University of Oslo) as a professor of natural history. He made several trips to along the Norwegian coast from Bergen to Lofoten to investigate the conditions of fisheries. He presented the results of these studies in Beiträge zur Fauna Norwegens which was published in 1843. At his death he bequeathed his estate and funded a trust (Rathkes legat) at the University of Oslo to use for study of Norway's natural conditions.
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