The parish church was established in 1580 – as an encomienda of the heir of Don Pedro de Gamboa.

Writing in 1582, Miguel de Loarca stated:

    ysla de bantayan. A la vanda del norte de a ysla de çubu apartada della como dos leguas esta la ysla de bantayan que terna oçho leguas de box y dos de ançho tiene çerca de mil yndios y son de vn encomendero ella y la ysla de Vohol aRiba diçho, la gente della es buena gente tratante tienen grande pesquerias que es ysla de heçha muçhos baxos tiene pesqueria de perlas aunqe poca cosa no se coje en ella sino a Millo y borona y no se coje ningun arroz por ques tierra toda de mal pais aunque llana algunos de los naturales desta ysla haçen sus sementeras en la ysla de çubu, como digo esta dos leguas de trauesia tiene muy buenos palmares y lo mismo se a de entender de todas las yslas de los pintados porque todas lellas abundan en gran cantidad de palmas.

Island of Bantayan. “About two leagues north of the island of Çubu lies the island of Bantayan. It is about eight leagues in circumference and two leagues wide, and has a population of about one thousand Indians; this and the above-mentioned island of Vohol are under the charge of one encomendero. Its inhabitants are well-disposed. They have large fisheries, for there are many shoals near the island. There is also a pearl-fishery, although a very small one. The land produces millet and borona, but no rice, for all the island has poor soil notwithstanding that it is level. Some of the natives of this island cultivate land on the island of Çubu, which, as I have said, is two leagues away. The island abounds in excellent palm-trees — a growth common to all the Pintados islands, for all of them abound in palms.”

He also wrote:

    Otra manera de esclauonia. Ay otro genero de señorio qe yntroduxo Vno que se llamaua sidumaguer qe Diçen que a mas de dos mill años qe fue que porque le quebraron vn barangay en languiguey donde el era natural ques En la ysla de bantayan qe si tenian los qe defienden, de Aquellos qe le quebraron el barangay si qdo mueren dexan diez esclauos le dauan dos y Al Respeto toda la demas haçienda, y esta manera de esclauonia. quedo yntroduçida en todos los yndios de las playas y no los tinguianes.

Another kind of slavery. “There is another kind of lordship which was first introduced by a man whom they call Sidumaguer — which, they say, occurred more than two thousand years ago. Because some men broke a barangay belonging to him — in Languiguey, his native village, situated in the island of Bantayan — he compelled the descendants of those who had broken his barangay to bequeath to him at their deaths two slaves out of every ten, and the same portion of all their other property. This kind of slavery gradually made its way among all the Indians living on the coast, but not among the Tinguianes.”

Writing in 1588, Domingo de Salazar reported: “The island of Bantayan is small and densely populated. It has more than eight hundred tributarios, most of them Christians. The Augustinians who had them in charge have abandoned them also, and they are now without instruction. This island is twenty leagues from Zubu.”

Some time in 1591, Bantayan’s population totalled 683 tributes representing 6732 persons.

Writing in 1630, Fray Juan de Medina noted: “Religious were established in the island of Bantayan, located between the island of Panay and that of Sugbú, but farther from that of
Panay. However, if one wishes to go to the island of Sugbú without sailing in the open sea, he may coast from islet to islet, although the distance across is not greater than one or one and one-half leguas. These Bantayan islets are numerous, and are all low and very small. The largest is the above-named one. When Ours acquired it, it had many inhabitants, all of very pleasing appearance, and tall and well-built. But now it is almost depopulated by the ceaseless invasions from Mindanao and Jológ.”

He goes on to say: “This island has a village called Hilingigay, which it is said was the source of all the Bisayan Indians who have peopled these shores, and whose language resembles that of Hilingigay.”

From 1635-1644, the Visayas were harrassed by the Moros. Stone walls and watchtowers were built throughout the Island-group for refuge and protection. Watchtowers were locally known as “Bantayan sa Hari” meaning “Watchtowers of the King”. In the course of their vigil after the Moros, it became a common expression for islanders to say “Bantayan, Bantayan” meaning “keep watch, keep watch”. This is how the island got his name, the watchtower ruins remain especially in the north of Madridejos and on Doong Island, part of the western archipelago.

On 4 January 1899, following the defeat of Spain in the Spanish–American War, a new government was born to the Philippines. With instructions from President McKinley, General Otis, who commanded the US Army in the Philippines, declared that the American sovereignty must be recognized without condition. This was the beginning of the American period.

This island-group did not taken any active part in the revolution against Spain or America. However, after the Filipino–American War, a reactionary group was organized, headed by Patorete of Santa Fe, then still a barrio of Bantayan. Their announced purpose was to resist the invaders, but the armed goons carried a campaign of terror burning the northern part of Santa Fe, plundering and forcing Capitan Miroy and Aguido Batabalonos to join them. This resulted in great fear and tension among the inhabitants.

The condition of the barrios, after the overthrow and immediately preceding the arrival of the Americans, in general, was very far from satisfactory. Sanitation was entirely a stranger; barrio life was dreadful. There were few signs of improvement among the people since their primitive ancestors.

The subdivision of the province of Cebu was developed utilizing the method introduced by Spain. A new provincial law had been enacted in 1895 and necessary appointments were then made. At that time, Bantayan was already organized as pueblo. Santa Fe was organized as such in 1911 and Madridejos in 1917. These pueblos were given a new corporate form under the Municipal Council chosen by a limited native electorate. For the local head of the administration, the title Presidente took the place of the former Gobernadorcillo or Capitan.

Committed to the task of administering the newly organized municipal governments were the first presidentes of the three towns comprising the island-group namely: Gregorio Escario for Bantayan, Vicente Bacolod for Madridejos and Casimiro Batiancila for Santa Fe. Political parties were formally organized since the early days of the American regime. Partido Liberal came towards the end of 1900. Pascual Poblete founded the Partido Independista in 1902.

During the administration of Governor-General Luke E. Wright (1904–1906), the public road policy was inaugurated. Little by little the stage trails were changed to roads of more durable construction. Late in 1913 the construction of Santa Fe—Bantayan road began and in 1918 the Bantayan—Madridejos road followed; both were completed in 1924.

Then and now, fishing and farming were important industries of the people, but from the year 1903 to 1925, weaving of piña cloth and the gathering of maguey fibre were very lucrative pursuits of the people. Over the years demand for these products weakened and died out. At about the same, hand embroidery termed as “spare time industry” came in. A good number of women adopted it and were actively engaged in it for some years. The local output was quite significant. In 1923, because of weak and unsettled market conditions, particularly in Manila, the business gradually disappeared.

Gregorio Zaide described the Philippine national characteristic as “pliant, like bamboo, bending in the wind without breaking”. This might explain the war-time actions of the then mayor Isidro Escario, who had himself rowed out to meet a fleet of Japanese warships where he treated with them: Bantayan was not invaded and the war basically passed it by.