He was the director and curator of the Musée zoologique de la ville de Strasbourg from 1882 to 1919. He headed the Zoologische Staatssammlung München from 1923 to 1927 and was Professor of Zoology in the Ludwig Maximilian University of Munich.
Ludwig Döderlein was born in Bad Bergzabern on March 3, 1855. He went to school in Bayreuth from 1864 to 1873. Both places were then part of the Kingdom of Bavaria. From 1873 to 1875 he studied natural sciences in the University of Erlangen-Nuremberg, where he also worked as an assistant to the German zoologist Emil Selenka in the summer of 1875. From 1875 to 1876 he took two semesters at the Ludwig Maximilian University of Munich.
After graduating, Döderlein moved to Alsace (which had been annexed by Prussia at the end of the Franco-Prussian War). There he completed his Doctorate of Philosophy in Mathematics and Natural Sciences at the University of Strasbourg on June 26, 1877. From 1876 to 1878 he worked for four semesters in the zoology department of the University of Strasbourg as an assistant to the German zoologist and phycologist Eduard Oscar Schmidt.
The prospects for an academic career were poor, so for a time, he worked as a schoolteacher in the Alsatian town of Mulhouse. There he met and befriended the Japanese student Kenji Oosawa (1852–1927), who was studying medicine and physiology at the University of Strasbourg. Oosawa arranged for Döderlein to be invited to Japan to work as a Professor of Natural History in the Faculty of Medicine of the newly established University of Tokyo. Döderlein accepted gratefully.
Döderlein was one of the first European academics invited to Japan during the Meiji Restoration era, when Japan was undergoing rapid modernization after the end of the isolation period (Sakoku). He stayed from 1879 to 1881 as an oyatoi gaikokujin ("foreign employee") professor. During this time, he collected and preserved marine life extensively, particularly fish, sponges, crustaceans, crinoids, sea urchins, cnidarians, and bryozoans. In addition, he also occasionally collected specimens of amphibians (including a giant salamander), mammals, birds, and plants. At first, he obtained most of his specimens from the fish markets and gift shops of Tokyo and the island of Enoshima. Later, he himself fished for specimens directly from Sagami Bay.