In 1844, the French sought to acquire Basilan, offering to purchase it from Spain, which was in financial straits. The plan came to naught. Afterwards, the Spaniards built a fort at a site called Pasangan or Pasangen. The fort was belonged to a field type or was a temporary fort. Pasangen was renamed to honor Queen Isabela II, following the visit of Ramon Lobo, the chief of the marine in Zamboanga and Cayetano Suarez, the governor of the district. Later that same year, Gov. Narciso Claveria ordered the construction of a stone fort, following the plan of engineer Emilio Bernaldez submitted in 1844. Construction lasted four years and the completed fort was named after Queen Isabella II.
In 1863, Basilan was separated from Zamboanga’s jurisdiction and constituted as the 6th Politico-militar distrito de Mindanao.
Nieto Aguilar (1894) describes the fort as “magnificent.” Situated 20 meters above sea level, the fortification overlooked the two entrances to the bay, formed by Basilan and Malamawi Island. To the fort’s east were the barracks. The fort had four bastions at the corner of its rectangular perimeter. It enclosed a well and had four structures for the corps of guards, the garrison personnel, the presidio, jail, artillery corps and the casa comandancia.
In the fort was the governor’s residence as well as that of his officials. It was also a naval station where the navy maintained small workshops for urgent repairs. It had a storehouse for coal near the shore. Total personnel: two officer, 50 men.
Outside the fort were built other structures, namely: a military infirmary, school, ayuntamiento (city hall), corps of engineers’ building, storehouses and dependencies of the naval station, barracks for the marine infantry, gunpowder storehouse, and the Jesuit church and convent. A naval hospital by the sea was established in 1879.
The fort and naval hospital were demolished in 20th century, when they were reduced to rubble by American bombs during World War II. The Basilan provincial capitol presently occupies the site of the demolished fort.
No remains are found.