It is also believed that Boljoon began as a pre-Hispanic settlement of Malay migrants who have found a route from Panay into the area. Based on the archives of the Augustinian Province of the Philippines, Boljoon was once a barrio of the town of Carcar. It was made independent in both its civil and ecclesiastical administration during the October 31, 1596 Congress of the congregation. Apparently, the town was first constituted as a parish before it was made into a municipality.
Historical records reveal at least five renditions of the name of the town. It is referred as Bolhon, Bolhong, Bolhoon, Bolhoong, and the current name and spelling of "Boljoon". A sixth one is that of Bolojon which was attributed to an error in copying. The area was apparently on the mission areas in Cebu when the first parish was founded in Bantayan in 1580 and possibly was erected as a parish only in 1692, based on existing records. It is not, however, a remote possibility that a church may indeed have been built before the close of the 15th century.
Four years after the creation of the suffragan diocese of Cebu in 1595, Fray Gaspar de San Agustin, OSA, in his Conquistas de las Islas Filipinas listed Boljoon as one of the many parishes under the jurisdiction of the Augustinians in the Province of Cebu in the year 1599. The area was already known for the cultivation of cotton from which native produced very good textiles. This may imply that cotton weaving and cultivation have already existed long before Fray Bermejo arrived in the town. Bermejo himself was said to have taught the local women cotton weaving and if Fray Gaspar's writings are to be considered, then Bermejo already found existing cotton cultivation and weaving industry in Boljoon.
Boljoon is 103 kilometers from Cebu City to the southeastern part of Cebu Province. It is bounded in the north by the town of Alcoy, on the east by the sea, on the south by Nueva Caceres (Oslob) and on the west by high mountains. It is famous for its crooked roads because of its elevated hill, which the town's people call "ILI". A small river irrigates its lands. The name of the town is derived for the local word "Bolho" which means springs of water.
The town is centuries old. Progress and modernity has altered the landscape although much of its natural features remain. The once verdant hills are now laid bald with the inroads of human civilization. Traces of its early-recorded history can be of the cemetery can still be seen. A few old houses built according to the design of the colonial period can still be found alongside modern houses.
Outside its boundary, Boljoon is known more a pilgrimage town in southern Cebu anything else, during the colonial period. According to oral tradition, pilgrims from as far as the town of Dalaguete visit the Virgin of Bolhoon during her annual feast to attend mass in the town's Catholic Church. The image of the Virgin, the center of devotion, is enshrined in the high altar of the church. It is several centuries old and is said to possess miraculous powers.
Boljoon was exempted from any tribute in 1894 and 1896. The population then was 7,694. Population increases was at such a slow rate due to the Muslim raiders which ransacked everything in the town and left all things on fire. Boljoon once contributed an annual rent of 80 cavans of borona to the convent of then San Agustin Church now the Basilica del Santo Niño de Cebu. This was later reduced to half in 1726 because it was found too burdensome for Boljoon, during the time of Bishop Sebastian de Foroinda, OSA (1718-1728), the ninth Bishop of the Diocese of Cebu.
Muslim raiders used to raid the settlement which often left the community in shambles. A Christian mission was also possibly erected in the place called the "Ermita" where priests perform religious services. The earliest Christian mission in Boljoon may have been established by the Augustinians in 1599. The Province of Cebu was then under their pastoral care and missionaries from the town of Carcar regularly visited by settlement in Boljoon. With the convention of the people to Catholicism, a provisional church may have been constructed but without a resident priest.
the first recorded residency of a priest in Boljoon was in 1692. Even with the presence of a priest in the settlement, the predations of the Muslim raiders upon the settlement continued, until the early 1800s. In fact, it was due to the incursions of the muslim raiders that a massive stone church was erected by the Missionaries, designed to withstand the raids. In addition, the Augustinians placed the church under the protection of the Virgin Mary and accordingly enshrined her image in the Church's altar.
The Roman Catholic parish of Patrocinio de Santa Maria is located in the town of Boljoon, Cebu. The Parish was said to have been founded simultaneously with the town after Boljoon was made capital of the Second Vicariate South of Cebu in 1692. Extant Archdiocesan records in fact trace the foundation of the parish to the year 1692, during the term of Bishop Agurto.
The forty-third parish priest of the Boljoon Parish Church in his list of Religiosos Agustinos Calzados Y PP Clerigos dated July 15, 1881 maintained that a church was previously erected in Boljoon 1599 under the administration of the Augustinians. The said church was allegedly destroyed by a fire of unknown origin in 1782. No records exist to support this claim but the Augustinian historian, Fray Isacio Rodriguez, OSA. was the usual procedure of the Augustinian provinces. In another document found in the archives of the Augustinian Province of the Philippines, that the Boljoon Parish was founded in 1549 which is disputed by historian since the Legazpi expedition arrived on April 24, 1565 or 44 years after Magellan's death and the first parish established in Cebu is Bantayan in 1580.
Some ecclesiastical historians believe that the Boljoon Parish was founded as a visita of Carcar. A visita is a 17th century ecclesiastical term referring to a settlement of Christians with a small chapel an "Ermita" with no resident priest and aggregated to a parish church. Records of the private council of the Augustinians on June 23, 1599 referred to Boljoon as a "convent and parish to Siaro (Carcar)". Writing about this private council, Fray Gaspar de San Agustin, OSA, mentioned BOljoon in the year 1599 as one of the eight parishes under the jurisdiction of the Augustinians in the coastal regions of the Province of Cebu, in towns with 300-400 inhabitants.
Records of the Archives of the Augustinian Province Congress of the Philippines indicated that it was the 1690 Augustinian Congress that established Boljoon as :independent Parish" having under its jurisdiction the Visitas of Oslob and Tañon, when the Father Provincial, Fray Francisco de Zamora, OSA, proposed the division of the administration of the Parish of Carcar due to its growth, both in the area of coverage and the number of parishioners. Boljoon was thus made independent both in its civil and ecclesiastical administration. As it happens, even to this day, a community becomes a parish first before it takes the status of a civil municipality. (Archives of the Augustinian Province of the Philippines, File no. 5 page 118)
On October 1, 1690, during the Interim Congress, the town of Carcar was "added" to Boljoon and Fray Nicolas de la Cuadra, OSA, "from the convent of Carcar" was assigned to Boljoon as its first Augustinian parish priest and prior on April 25, 1692. It must be pointed out that since October 1, 1690, the Father Provincial of the Augustinians reserved the right to designate and appoint the parish priest of the Parish of Boljoon since its creation as an "independent parish" from Carcar and that whomever he appoints shall be considered as appointed by the Congress. (Archives of the Augustinian Province of the Philippines, file no. 5 page 160)
Due to the lack of priests, the church was turned over to the Jesuits on September 27, 1737, upon the recommendation of the intermediate chapter of 1732. In the year 1747, the General of the Augustinians Order proposed the recovery of the parishes left off in the Visayas. The Parish of Boljoon was returned by Jesuits in exchange for "Liloan", Cotcot and Maraling", the last Augustinian Parish Priest of Boljoon, Fray Leandro Moran, OSA, turned over the administration of the parish to the Archbishop of Cebu on July 1, 1948. (Archives of the Augustinian Province of the Philippines File no. 298 page no. 14)
The first secular parish priest of Boljoon, Fr. Zacarias Suñer, assumed his post 1958 during the time of Julio R. Cardinal Rosales, Archbishop of Cebu, based on Archdiocesan records. It was not clear as to reason for the delay when the last Augustinian Parish priest of Boljoon. Fray Leanfdore Moran, OSA, turned over the administration of the parish to the Archbishop of Cebu on July 1, 1948. The appointment of Archbishop Reyes in 1949 as Head of the Archdiocese of Manila may be one of the reasons. His successor, then bishop later cardinal Julio R. Rosales from Tagbilaran assumed the post as the Archbishop in 1950.
The Boljoon Church is the oldest remaining original stone church in Cebu. In 1999, the National Historical Institute declared it a National Historical Landmark. The following year, the National Museum declared it as a National Cultural Treasure.