By the mid-nineteenth century, the south of Mindanao and the south of the Philippines in general, were a usual haven of Muslim pirates, who devastated the coasts of the archipelago in search of booty and prisoners that they later sold in the market of Jolo. The Spanish government proposed the elimination of the pirates. To accomplish this, several expeditions were carried out against the pirate havens starting in 1843. One of the major expeditions was led by Narciso Clavería y Zaldúa, the governor-general of the Spanish colony, in early 1848. He organized a fleet of 19 warships at Manila under Brigadier José Ruiz de Apodaca including 2 steamers, 2 schooners and 3 brigs, plus several smaller vessels, including gunboats and feluccas. Three regular infantry companies under Lieutenant Colonel Arrieta were embarked on these ships on 27 January. Two other companies, a beefeater battalion, a contingent of police, an artillery detachment, and some engineers and workers were later embarked. The flagship of the fleet was the steamer Reina de Castilla. The fleet was joined by several transports at Daitan, and, on 17 February, set sail to the major pirate base of Balanguingui. The fleet was reinforced on the way by several Filipino local vessels called vintas and 150 auxiliaries of Zamboanga.
Balanguingui was a small island with an area of 6 square miles, covered with mangroves and jungle. The ground was so flat and swampy that when the tide rose, just a few sandbanks remained dry. Four forts stood over these sandbanks, surrounded by some houses built on stilts. A shallow channel divided the island in two portions, also spreading into several branches which penetrated inside the ground, making Balanguingui a swampy maze. The forts were known by the names of Sipac, Balanguingui, Sungap and Bocutingol. The first two were the biggest, and were located at the tip of the largest estuary. Their walls were built with tree trunks ranging from 2 to 3 feet in diameter and from 18 to 20 in height, and were reinforced by fences and stone embankments.