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The name Zamboanga was derived from the Malay word Jambangan, meaning a pot or place of flowers. Historically, Zamboanga was the capital of the Moro province, which comprised five districts, namely: Cotabato, Davao, Sulu, Lanao, and Zamboanga. In 1940, these districts became individual provinces. Zamboanga City became the capital of Zamboanga province. Soon after the Second World War, the provincial capital was transferred to Dipolog. After that, Molave was created as the provincial capital by virtue of RA 286 dated June 16, 1948.

Zamboanga del Sur was carved out from the former Zamboanga province that encompassed the entire peninsula in the southwestern Mindanao on September 17, 1952 by virtue of Republic Act 711. As the 52nd province of the Philippine Republic, it originally consisted of 11 towns, which later expanded into 42 municipalities and one city, Pagadian, its capital.

The province was sub-divided into three congressional districts, with 11 municipalities and one city in the first, 15 municipalities in the second, and six towns in the third. In 1990, Executive Order 429 reorganized the administrative setup of Region IX and identified Pagadian City as the new regional center. The actual transfer of the regional offices of national government agencies, however, has yet to be implemented.

Political developments in February 2001 saw another major change in the territorial jurisdiction of Zamboanga del Sur. its inhabitants voted to create a new province out of the third congressional district, named Zamboanga Sibugay. The mother province is now left with 26 municipalities and one city with 681 barangays.

Batanes Province