The region is located on the eponymous Zamboanga Peninsula of the island of Mindanao, that lies between the Moro Gulf (part of the Celebes Sea) and the Sulu Sea. Along the shores of the peninsula are numerous bays and islands. The peninsula is connected to the rest of Mindanao through an isthmus situated between Panguil Bay and Pagadian Bay. Its territory consists of the three Zamboanga provinces and the city of Zamboanga, and the boundary between the peninsula and mainland is artificially marked by the border between the provinces of Zamboanga del Sur and Lanao del Norte.
During the ancient era, the southern Philippines, particularly the Sulu Archipelago and surrounding coastal regions was under the influence of the Javanese Majapahit Empire.
During the late 15th century and early 16th century, Malay missionaries spread Islam in the southern Philippines. Sharif Kabungsuwan, a Johore-born missionary of Malay and Arab descent established the Sultanate of Maguindanao, which the entire island of Mindanao is named after. The Sultanate also occupied nearly the entire island, stretching from the Zamboanga Peninsula to modern-day Davao City, while the Sultanate of Sulu occupied the Sulu Archipelago, parts of Sabah and Palawan. Magauindanao's sultans provided Mindanao fierce armed resistance against the Spanish occupation, especially under the lead of Muhammad Kudarat. They soon allied themselves with the Sulu Sultanate. The Muslim natives of the region were collectively known as Moros by the Spanish, meaning "Moor", though the Iberian Moors and the Philippine Muslims had little cultural connection outside of following Islam. A large chunk of the Spanish-Moro Conflict, the war between the Spanish conquerors and Mindanao's Muslim natives took place in the Zamboanga Peninsula.
In 1569 Zamboanga was chosen as the site of the Spanish settlement and garrison on La Caldera (now called Barrio Recodo). Zamboanga was one of the main strongholds in Mindanao, supporting colonizing efforts in the south of the island and making way for Christian settlements. It also served as a military outpost, protecting the island against foreign invaders and Moro pirates and their Chinese allies.
The Zamboanga Peninsula played a central role in the Spanish-Moro conflict. It was the site of constant battling between Spanish soldiers and Moro pirate raids. While the Spanish settlers successfully established churches in the region, they suffered heavily at the hands of Moro raiders, and had to repeatedly withdraw from the region. While the Spanish achieved a tactical victory, but launching several attacks against the Sultanate of Sulu, constant fighting and attacks persisted, giving the Moros a psychological victory.
After the United States annexed the Spanish East Indies in 1898, the Peninsula hosted a briefly independent state called the Republic of Zamboanga. It was incorporated by the Insular Government into the Moro Province, which consisted of the Central and Western parts of Mindanao and the Sulu Archipelago. The name and status of Moro Province were changed to the Department of Mindanao and Sulu on August 16, 1916, causing Zamboanga to become a separate province.
In 1942, the Zamboanga Peninsula along with the rest of the Philippine Islands was occupied by the Empire of Japan at the beginning of the Second World War. The Peninsula was liberated in 1945 by joint American and Philippine Commonwealth forces fighting against the Imperial Japanese Army.
On 6 June 1952, the province was partitioned into Zamboanga del Norte and Zamboanga del Sur, while the chartered city of Zamboanga became an independent, extraprovincial unit.
Together with the Sulu Archipelago, the provinces that formerly made up Zamboanga Province were re-organised into Region IX by order of Presidential Decree No. 1 as part of the Integrated Reorganization Plan of President Ferdinand Marcos, that was signed in September 24, 1972.
From 1975 to 1989, the old Region IX (Western Mindanao) was further divided into two sub-regions by Presidential Decree No. 8233 dated August 21, 1975. Sub-Region IX-A consisted of Basilan, Sulu and Tawi-Tawi with Jolo, Sulu, as the sub-regional center, while Sub-Region IX-B consisted of the provinces of Zamboanga del Norte and Zamboanga del Sur, with the chartered city of Zamboanga City as the sub-regional centre.
In 2001, Zamboanga Sibugay, was created from the province of Zamboanga del Sur with Ipil as the seat of government with the virtue of Republic Act No. 8973.
In the same year, the residents of Basilan opted to join the Autonomous Region in Muslim Mindanao (ARMM) in a plebiscite. However, the citizens of the capital, Isabela, did not want to join so the city remained a part of this region as a result of Executive Order No. 36.
In 2004, Pagadian officially became the Regional Center for Region IX- Zamboanga Peninsula, despite opposition from Zamboanga City, the former Regional Center.
Executive Order (EO) 429 was issued in 1990 by President Corazon Aquino which provided for the reorganization of the administrative regions in Mindanao. It declared that Western Mindanao would comprise Zamboanga City, Lanao del Norte, Misamis Occidental, Zamboanga del Sur, Zamboanga del Norte, Basilan, and the cities comprising those provinces. It also declared that Pagadian City shall serve as the new regional center.
However, President Fidel Ramos issued EO 325 in 1996 which reorganized the Regional Development Councils (RDCs). The Implementing Rules and Regulations (IRR) of EO 325 declared Pagadian City as the regional center in Western Mindanao.
In 2001, President Gloria Macapagal-Arroyo signed EO 36 which reorganized and renamed Western Mindanao to Zamboanga Peninsula. It was silent on the issue of regional government centers. Memorandum Circular No. 75, signed in 2004 by Executive Secretary Eduardo Ermita, directed the transfer of regional offices from Zamboanga City to Pagadian citing EO 429 as its legal basis.
A moratorium on the transfer under Memorandum Circular No. 11 was issued on December 22, 2010 citing the high economic and social costs that the employees were experiencing in maintaining two residences and in fully transferring to Pagadian. It further directed all regional offices that are already in Pagadian to continue their operations.
On March 3, 2011, the Regional Development Council IX endorsed Pagadian as the regional center of Zamboanga Peninsula.
National Economic and Development Authority Regional Director Arturo Valero stated that “even if Zamboanga City is not the regional center, the city will still grow” and that the city should better focus on being a commercial and industrial center.
Zamboanga Peninsula comprises 3 provinces, 1 independent, chartered and highly urbanized city, 4 component cities, 67 municipalities and 1,904 barangays.
Isabela City is a component city and capital of the province of Basilan. It continues to be under the jurisdiction of Basilan for the administration of provincially devolved services and functions. But for the administration of regional services, the city is part of the Zamboanga Peninsula Region despite the rest of Basilan being under the authority of the Autonomous Region in Muslim Mindanao.
Isabela was the southernmost outpost of the Spanish in the Philippines until the fall of Jolo in 1878. Having hosted Catholic residents since 1637, and a Spanish Fort (destroyed in World War II) since 1848, it was likewise the primary naval base of the Spanish in Mindanao until 1899. Named after Queen Isabella II, the city is the southernmost predominantly Christian enclave of the Philippines, and serves as an entry point for trade and commerce of Basilan island.
Dapitan is also known as the "Shrine City in the Philippines" because the place where José Rizal, the National Hero, was exiled. It is also known for the old St. James Parish and the beach resort of Dakak.
Dipolog, capital of Zamboanga del Norte, is known for their orchids, thus called "Orchid city of south" or "Orchid City" because of the abundant wild Dipolog orchids. They have their nature spots and historical spots, such as Dipolog Cathedral, Dipolog Boulevard, Cogon Park, Japanese Park, Magsaysay Park, the Sungkilaw Falls, and the 3000 steps to Linabo Peak.
Pagadian is known as the "Little Hong Kong of the South" because of its topographical feature that is reminiscent of Hong Kong. It also has an affluent Chinese community that officially celebrates the Chinese Lunar New Year.
Zamboanga City is the only Independent, chartered city and highly urbanized city in the region. The city is the lone member of BIMP-EAGA in the Zamboanga Peninsula. Zamboanga City generates more than half of the economy of the region. It also has the largest airport and seaport and the city in the region with most investors.
It has the first export-processing zone in Mindanao. Farming and fishing are the main economic activities of the region. It also has rice and corn mills, oil processing, coffee berry processing and processing of latex from rubber. Its home industries include rattan and furniture craft, basket making, weaving and brass work.
The region has vast forest resources and previously used to export logs, lumber, veneer and plywood. Mineral deposits include gold, chromite, coal, iron, lead, and manganese. Among its non-metallic reserves are coal, silica, salt, marble, silica sand, and gravel. Its fishing grounds are devoted to commercial and municipal fishing. It has also aqua farms for brackish water and freshwater fishes.
The economic fulcrum of the region lies at the center of the peninsula that is the area connecting Ipil and Liloy. It is the fastest economic activity of the region. The 30 kilometer link between the north and the south would act as the main artery of economy in the region.