One can trace the intellectual and institutional genealogy of social anthropology back to the beginnings of the Imperial Academy of Sciences. Its co-founder and first president Joseph Freiherr von Hammer-Purgstall was not only a philologist and historian, but also an ethnographer of the Middle East. The physician Karl Freiherr von Rokitansky, president of the Academy from 1869-1878 and co-founder of the Anthropological Society of Vienna, was also strongly committed within the Academy to the development and institutionalization of the discipline in the broadest sense, which at that time included physical anthropology, prehistory and early history, and ethnography. 1897 saw the founding of the Commission for the Study of American, Asian and African Languages, which was renamed the Commission for the Study of Illiterate Languages of Non-European Peoples in 1910, becoming one of the institutional predecessors of ISA. Other predecessor institutions were the Northern Arabian Commission and the Southern Arabian Commission, which were later merged into the Arabian Commission; and the Commission for Research in World War I Prison Camps, which was initiated by Rudolf Pöch. It was merged with the Commission for the Study of Illiterate Languages in 1938 and renamed the Ethnological Commission in 1961. During these years, the head of the University Institute of Ethnology, Father Wilhelm Koppers, was also Full Academy Member. The Arabian Commission and the Ethnological Commission were merged in 1993 and renamed the Commission for Social Anthropology in 1995.

Just as anthropology was an important part of the Academy’s scientific activities from the beginning, Arabian research was a central focus of social anthropology in Vienna from the very beginning, which was later continued by Walter Dostal and Andre Gingrich (Full Academy Members), Johann Heiss, and Marieke Brandt at ISA. ISA’s two other regional areas in Asia – the Tibetan and Mongolian regions and Southeast Asia – also have a long history at the Academy. As an Academy Member, the ethnologist and founder of Southeast Asian Studies, Robert von Heine Geldern, internationalized ethnological and archaeological research on Asia, which was later actively developed further at ISA by Helmut Lukas and now Martin Slama and Judith Bovensiepen. Walter Dostal, himself a student of Heine Geldern, connected not only the long-standing Southwest Arabian tradition at the ÖAW, but also the almost equally long-standing research on Tibet in Vienna with a historical-anthropological approach. Together with Academy Member Ernst Steinkellner, who revolutionized philological Tibet research and was director of the Institute for the Cultural and Intellectual History of Asia from 1998 to 2006, he facilitated the first anthropological Tibet projects at the ÖAW (with Hildegard Diemberger and Guntram Hazod), through which the Commission for Social Anthropology became staffed for the first time. This regional focus is continued today by Hubert Feiglstorfer, Christian Jahoda, Nina Lang and Stephan Kloos at ISA.

Andre Gingrich, the founding director of the institute in its current form, was awarded the Wittgenstein Prize in 2000, with which he investigated local identities and wider influences in the Middle East, Tibet and Southeast Asia with a young team for more than six years. In 2003 he took over as chair of the Commission for Social Anthropology from Full Academy Member Walter Dostal. In 2007, after the Wittgenstein project came to an end, the Academy transformed the Commission into a research unit and took over a core of the Wittgenstein staff. In 2009, the research unit became the current Institute for Social Anthropology, which was granted permanent status in 2011 after a successful evaluation. Since then, ISA has developed into one of the most important social anthropological research institutes not only in German-speaking countries, but in Europe and beyond. Andre Gingrich retired at the beginning of August 2019, and in October 2019 Stephan Kloos was appointed by the Presidential Board of the Austrian Academy of Sciences to lead the institute on an interim basis. Since fall 2023, Judith Bovensiepen has been the new director of the ISA.