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During the Middle Ages, Afgooye and much of the surrounding area in southern Somalia was governed by the Ajuuraan State. The city later came under the administration of the Geledi Sultanate in the 1800s. The Istunka martial arts festival that is held annually in the town during the Somali new year dates from this period.
At the turn of the 20th century, Afgooye was incorporated into Italian Somaliland. The Italians occupied the town in 1908 and in the process abolished the local slave market. There was also a station in Afgooye on the Mogadishu-Villabruzzi Railway, which connected the city to the capital Mogadishu.
Afgooye is inhabited by numerous Somali clans, as well as some ethnic minority groups. The Digil and Mirifle (Rahanweyn) sub-clans, the Wacdaan Cismaan sub-clan of the Mudulood, Loobage and the Gaaljecel and Garre are especially well represented.
- Abdullahi Issa, Prime Minister of the Trust Territory of Somalia
- Mohamed Osman Jawari, Speaker of the Federal Parliament of Somalia
- Mustafa Mohamed Moalim, Chief of the Somali Air Force School and Operations
- International Institute for Mesopotamian Area Studies, Monographic journals of the Near East, (Undena Publications: 1981), p.78
- Lee V. Cassanelli, The Shaping of Somali Society: Reconstructing the History of a Pastoral People, 1600-1900, (University of Pennsylvania Press: 1982), p.102.
- Lee V. Cassanelli, The Shaping of Somali Society: Reconstructing the History of a Pastoral People, 1600-1900, (University of Pennsylvania Press: 1982), p.271.
- I.M. Lewis, A Modern History of Somalia, fourth edition (Oxford: Currey, 2002), p. 87
- Mooge, Ahmed; Gallagher, Patrick (22 October 2010). "Civilian casualties mount in Mogadishu". Los Angeles Times.
- "Somali al-Shabab militant stronghold Afgoye 'captured'". BBC. 25 May 2012. Retrieved 1 June 2012.
- "Somalia - City & Town Population". Tageo. Retrieved 27 September 2013.
- "Regions, districts, and their populations: Somalia 2005 (draft)". UNDP. Retrieved 21 September 2013.
- Luling, Virginia (2002). Somali Sultanate: the Geledi city-state over 150 years. Transaction Publishers. ISBN 0-7658-0914-1.