Manila began as a Muslim settlement at the mouth of the Pasig River along the shores of Manila Bay. The name came from the term maynilad, literally "where there is nilad." Nilad is a white-flowered mangrove plant that grew in abundance in the area.

In the mid-16th century, the area of present-day Manila was governed by three rajahs, or Muslim community leaders. They were Rajah Sulayman and Rajah Matanda who ruled the communities south of the Pasig, and Rajah Lakandula who ruled the community north of the river. Manila was then the northernmost Muslim sultanate in the islands. It held ties with the sultanates of Brunei, Sulu, and Ternate in Cavite.

In 1570, a Spanish expedition ordered by the conquistador Miguel López de Legazpi demanded the conquest of Manila. His second in command, Martín de Goiti departed from Cebu and arrived in Manila. The Muslim Tagalogs welcomed the foreigners, but Goiti had other plans. The Spanish force of 300 soldiers marched through Manila and a battle was fought with the heavily armed Spaniards quickly defeating the native settlements. Legazpi and his men followed the next year and made a peace pact with the three rajahs and organized a city council consisting of two mayors, 12 councilors, and a secretary. A walled city known as Intramuros, at the southern banks of Pasig River was built to protect the Spanish colonizers. On June 10, 1574, King Philip II of Spain gave Manila the title of Insigne y Siempre Leal Ciudad ("Distinguished and Ever Loyal City").

In 1595, Manila was proclaimed as the capital of the Philippine Islands and became a center of trans-Pacific trade for more than three centuries. For example, the famous Manila galleons sailed between Manila and the port of Acapulco in today's Mexico. These Manila galleons carried silver and other precious metals from the New World to Manila to purchase goods and raw materials from throughout Asia — for example, spices transshipped from the Spice Islands to the south, and porcelain, ivory, lacquerware and processed silk cloth from China and Southeast Asia. Some of these Asian goods were used in Mexico, however, most of the cargo was transshipped across Mexico for delivery to Spain, to be sold in European markets.

There was a brief British occupation of Manila from 1762-1764 as a result of the Seven Years' War, which was fought between France and Britain. Spain became a British enemy when it sided with France due to ties between their royal families. The British Occupation was confined to Manila and Cavite while Simón de Anda y Salazar, acting as a de facto Spanish governor general, kept the countryside for Spain with the help of Filipino soldiers. The Indian soldiers known as Sepoys, who came with the British, deserted in droves and settled in Cainta, Rizal, and explains the uniquely Indian features of generations of Cainta residents. French mercenaries who came with the British also settled in various locations around Manila

U.S. Troops invaded Manila in 1898 and waged war with the Spaniards and Filipinos in the Spanish-American War and the Philippine-American War. Following the defeat of Spain, U.S. forces took control of the city and the islands in one of the most brutal and forgotten chapters of Philippine American history

The American Navy, under Admiral George Dewey, defeated the Spanish squadron in the Battle of Manila Bay on May 1st, 1898. Admiral Dewey testified that after the battle the Spanish Governor wished to surrender to the Americans rather than the Filipinos, whom he feared

Having just won their independence from Spain, the Filipinos were fiercely opposed to once again being occupied. Emilio Aguinaldo proclaimed the First Philippine Republic at the Malolos Congress and had begun to build the foundations for an independent nation. Admiral Dewey, however, claimed he never recognized the Philippine Republic, as he did not have the authority to do so and did not consider it an organized government. [1]

American high command at that time was headed by General Otis who ordered invasion and occupation. By that time the Filipino troops had taken classic defensive positions around Manila to attempt to keep them out. However, the poorly armed, ill-trained soldiers could not compete with the superior firepower of the Americans and they lost and were severely beaten; so much so that it has been reported that the dead were used as breastworks.[citation needed]

Under the command of Aguinaldo the Filipinos began a guerrilla campaign to resist the new occupiers. This campaign had limited success in the early days following the initial occupation of the Americans although any successes were short-lived. The replacement of General Otis by General MacArthur began an extensive campaign to suppress the local population.

This campaign by the USA has been reported as being a particularly bloody suppression with wild reports of commanders ordering the murder of everyone over 10 years old. Several books have been written on this war and it's implications for both the local peoples and the US. These books are largely hostile to the US:

In the Treaty of Paris in 1898, Spain handed over the Philippines to the United States of America for US$ 20,000,000 and ending 333 years of Spanish rule in the islands

American combat units were ordered to withdraw from the city and all military installations removed on December 30 , 1941. Manila was declared an open city by President Manuel L. Quezon, to spare the city from death and destruction. Quezon issued a decree enlarging the safe zone to include outlying areas of Manila as safe zones, establishing the new administrative jurisdiction called Greater Manila.

The post of mayor of Greater Manila was given to Quezon's former Executive Secretary, Jorge B. Vargas. On the evening of New Year's Day of 1942, a Japanese courier delivered notice to Vargas that Japanese forces already bivouacked at Parañaque would enter Greater Manila the following day. From 9 am to 10 am of January 2, Japanese imperial forces marched into the City of Manila.

Vargas was tasked to hand over to the new authorities Greater Manila and present the remaining Filipino leaders to Japanese authorities. Vargas and the Filipino leaders present were asked to choose three options; (1) a purely Japanese military administration, (2) a dictatorial government run by a Filipino under General Artemio Ricarte who went on self-exile to Japan after the Filipino-American war, or (3) a government by commission selected by Filipinos. Vargas and the local leaders chose the third option and established the Philippine Executive Commission to manage initially Greater Manila, and was later expanded to cover the whole of the Philippines.

Vargas assumed the chairmanship of the Philippine Executive Commission and appointed to the post of Mayor of Greater Manila in 1942, Leon G. Guinto Sr., a Secretary of Labor under the Philippine Commonwealth administration of President Manuel L. Quezon. Guinto held the position of Mayor of Greater Manila until the liberation of the city.

Under Guinto's war-time administration, the City of Manila that was expanded to Greater Manila included districts such as; "Bagumbayan" means New Town (South of Manila), "Bagumpanahon" means New Era (Sampaloc, Quiapo, San Miguel and Santa Cruz), "Bagumbuhay" means New Life (Tondo), "Bagong Diwa" means New Order (Binondo & San Nicholas), the then newly established Quezon City was collapsed and divided into two districts, while the municipalities of Caloocan, Las Piñas, Malabon, Makati, Mandaluyong, Navotas, Parañaque, Pasay, and San Juan became districts of Manila.

On October 20, 1944 American General Douglas MacArthur fulfilled a promise to return to the Philippines (see Battle of Leyte). From February 3 to March 3, 1945, after the climactic battle at Intramuros ended, the thoroughly devastated city of Manila was officially liberated. Allied Filipino & American troops did not reach the city in time to prevent the Manila Massacre though.