Zamboanga City is the proverbial melting pot, a product of the blending of many cultures from Chinese, Malaysian, Spanish, Japanese, Arabic and Caucasian blood.

Zamboanga was founded in 1635 by the Spanish as a military base for campaigns against the Moro. The early Malay settlers called the region "Samboangan". In one of the earliest Spanish maps, "Samboangan" meant "docking point" from the word "sabuan" the wooden pole used by the Samals and Badjaos in pushing their vintas on shallow waters. June 23, 1635 marked the change of the name of the place from "Samboangan" to its present name, ZAMBOANGA.

For almost three centuries, the Spaniards held over what is now Zamboanga City with Fort Pilar as the center of settlement. The presence of the Spaniards amidst many Filipino ethnic groupings resulted in the development of a unique dialect - chavacano - a mixture of Spanish and the native dialects which is still the predominant medium of communication in the city today.

In 1898,a year after the Treaty of Paris, the Philippines were ceded to the United States of America and the Americans occupied Zamboanga City. During the U.S. administration (1898–1935) of the Philippines the city was modernized. In 1901, the settlement was formally organized into a municipality.

From 1903 to 1913, Zamboanga was the capital of the Moro Province which was the whole of Mindanao, comprising five districts, namely: Cotabato, Davao, Sulu, Lanao and Zamboanga. The period led to the construction of its present day City Hall. It was then the Provincial Capitol building which housed the office of the Governor, General John "Black Jack" Pershing.

On September 15, 1911, the governing body of the Moro Province, the legislative council, passed Act. No. 272 converting the municipality of Zamboanga into a city with a commission form of government.

On October 12, 1936, Zamboanga became a chartered city under Commonwealth Act. No. 39 with the island of Basilan as part of the territory, thus making Zamboanga the largest city in the world.

During World War II, the city was held by the Japanese.

The city was largely rebuilt after the severe devastation of World War II, of which a few buildings remain that reflect its glorious past.

On November 22, 1983, Zamboanga was declared a highly urbanized city.

Its mountainous backdrop combine with a climate that is cooler and less humid than that of Manila and other sections of the country, to make it a favourite tourist spot.