The earliest Spanish accounts refer to Iligan(or Yligan/Elegin) as the name of the settlement found at the mouth of the river that bears the same name(also Tambacan to many people).It was this same settlement that the early Jesuits in Mindanao came upon sometime in the 1630s. Around the 18th century, Iligan referred to the large military province or corregimiento, which comprised the present-day provinces of Lanao, Misamis Occidental, Zamboanga del Norte, and portions of Misamis Oriental. When Ferdinand Blumentritt cited the earlier ethnographic accounts pointing to Subanos as the inhabitants of Iligan he must have referred to the corregimientos Misamis-Zamboanga side, concededly Subano territory till the present.
The Padres Recoletos are reported to have introduced Christianity in the area ahead of the Jesuits, the work having been begun by Fray Nicolas de San Juan who was the visitador of Bayug Island some three kilometers east of the present Poblacion. This was in 1626. There is reason to believe, however, that the natives of Bayug(whom I suspect to be ancestors of the Higa-onons of Barangay Rogongon, this city) had their first contacts with Christianized natives with the conquest of their territory ( in all likelihood towards the end of the 16th century) by Pedro Manuel Manook, a Dapitan warrior of considerable military and navigational skills. He showed Legaspi the way to the petty-kingdoms of Luzon. Both the Jesuits and the Recoletos will later be engaged in a scandalous battle fought in ecclesiastical and governmental courts to gain control over Iligan and neighboring areas.
Iligan has been traditionally used by both Spanish and American colonizers as the launching pad of their pacification campaigns against the Lanao "Moros." Thus, for more than two centuries, Iligan was practically a garrison town defended largely by Pampango and Boholano conscripts. It is reported that at the turn of the 20th century, Iligan had a population of only 3,000.
Like the other coastal settlements, Iligan was also constantly attacked by the Muslims, a retaliatory action against the Spanish intruders. In 1639, on order of Gov. Gen. Sebastian Hurtado de Corcuera, Captain Francisco de Atienza y VaƱez, a tried warrior from Toledo, Spain, constructed six collapsible boats, each capable of carrying 50 to 100 men, to be assembled at Lake Lanao. As in charge of Iligan, and after receiving suggestions from Fr. Fray Agustin(known as Padre Capitan) on the military technique and strategy against the Muslim strongholds, he led as expedition to Malanao. After the fall of Marawi to the Spaniards, the Muslims continued to harass the enemy on the sea and on land. They even cut off the supply route from Iligan, causing Atienza to pull back and fortify Iligan from the increasing Muslim attacks.
In later years, the poblacion of Iligan began to sink. Another fort was built by Gobernadorcillo Remigio Cabili and the town was transferred to its present site.
After Corcuera's rule, the Maranao were left to themselves, almost to the end of the Spanish rule. With Iligan as springboard, the Spanish troops were again sent to Marawi in 1891. Governor-General Eulogio Despujol continued the campaign to subjugate the lake region. However, it was Governor Ramon Blanco who established the Spanish power in the region. In 1895, Blanco with 5000 men under the immediate command of General Parrado, landed in Iligan and succeeded in conquering the Muslim cottas and the stronghold of Marahui, known as the strongest in Lanao.
In 1896, when the Philippine revolution broke out, an insurrection also occurred in Iligan. Three years later, the gobernadorcillo abandoned the town, and Captain Hilarion Ramiro took over the reins of the government. He received the Americans forces under the command of Captain Smith who landed at Iligan in 1900.