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Mindanao is divided into 5 administrative regions and 1 autonomous region, which is subdivided into provinces and independent cities.

Zamboanga Peninsula
Zamboanga Peninsula, numerically designated as Region IX, formerly Western Mindanao, is located in the landform of the same name. It consists of the provinces of: and the independent city of: Isabela City is part of Basilan which is in Bangsamoro Autonomous Region in Muslim Mindanao but for the administration of regional services, the city is part of the Zamboanga Peninsula Region. The region's administrative center is Pagadian and the whole region used to be a single province named Zamboanga.
 * Zamboanga del Norte
 * Zamboanga del Sur
 * Zamboanga Sibugay
 * Zamboanga City

Northern Mindanao
Northern Mindanao, numerically designated as Region X consists of the provinces of: and the independent cities of: Cagayan de Oro City serves as the region's administrative center.
 * Bukidnon
 * Camiguin
 * Lanao del Norte
 * Misamis Occidental
 * Misamis Oriental
 * Cagayan de Oro
 * Iligan

Davao Region
Davao Region, numerically designated as Region XI consists of the provinces of: and the independent city of: Its territory used to be a single province of Davao. Davao City serves as the region's administrative center.
 * Davao de Oro
 * Davao del Norte
 * Davao del Sur
 * Davao Occidental
 * Davao Oriental
 * Davao City

Soccsksargen
Soccsksargen, numerically designated as Region XII, consists of the provinces of: and the independent city of: Koronadal serves as the region's administrative center. In 2019, Cotabato City was once part of the region until it was transferred to Bangsamoro Autonomous Region in Muslim Mindanao. 63 barangays of Cotabato while part of it, voted to join the Bangsamoro Autonomous Region.
 * Cotabato
 * Sarangani
 * South Cotabato
 * Sultan Kudarat
 * General Santos

Caraga
Caraga, numerically designated as Region XIII consists of the provinces of: and the independent city of: Butuan serves as the region's administrative center.
 * Agusan del Norte
 * Agusan del Sur
 * Dinagat Islands
 * Surigao del Norte
 * Surigao del Sur
 * Butuan

Bangsamoro Autonomous Region in Muslim Mindanao
The Bangsamoro Autonomous Region in Muslim Mindanao (BARMM) is a special region which covers the territories predominantly populated by Muslims. Bangsamoro has its own government unlike almost all the other regions in the country. It consists of the provinces of: and the independent city of: Cotabato City serves as the region's administrative center. Isabela City, while part of Basilan, is under the jurisdiction of Zamboanga Peninsula. BARMM also includes the 63 barangays of Cotabato known as the Special Geographic Area (SGA).
 * Basilan
 * Lanao del Sur
 * Maguindanao
 * Sulu
 * Tawi-Tawi
 * Cotabato City