In August of 1795, Father Juan Mariner of Mission San Diego, explored the back-country of San Diego County looking for a possible site for a new mission. Father Mariner recommended a site in the Pala Valley because of an abundance of water and his regard for the Indian population. Pala was selected for the site, but then it was decided to locate the mission closer to the coast, and thus, San Luis Rey de Francia was founded in its current location.
Mission San Luis Rey expanded its influence north and east, including the Pala Valley. Mission San Luis Rey's first record of construction at Rancho de Pala was in the annual report of 1810. This construction was a granary and other buildings soon followed. As Mission San Luis Rey began to flourish, Father Peyri felt it was necessity to establish an asistencia near Pala because it was the natural congregating place for a large native population. A chapel was built in 1816.
Within two short years, the quadrangle was complete, two granaries were built, and two apartments were built, one for men and boys and one for women and girls. By 1818, a small town had began. Father Peyri had an aqueduct built to supply water to the mission. By 1821, the mission only lacked a resident priest to make the asistencia a full mission. Mission Pala had reached its peak prosperity by 1827 when Father Peyri described Mission Pala, "At a distance of seven leagues toward the northeast, ... (San Luis Rey) has a station called San Antonio de Pala with a church, dwellings, and granaries and with a few fields where wheat, corn, beans, garbonzoes, and other leguminous plants are grown. There is also a vineyard and an orchard of various fruits and olives, for which there is sufficient irrigation..."
Secularization came to the asistencis in the mid 1830s and as at other missions, Pala began a decline. On August 22, 1835, Mission San Luis Rey and Mission San Antonio de Pala were turned over to Pio Pico and Pablo de la Portilla, two commissioners appointed by Governor Figueroa. Because of Pala's remote location, the Indians were able to maintain the chapel and grounds for a time, but eventually the condition of the Indians deteriorated and by 1840, their condition was described at "pitiable." Also in 1840, Pio Pico was relieved of his office as administer of San Luis Rey and its properties. He refused to relinquish possession of the missions which resulted in a violent opposition by the Indians. On May 18, 1846, fearing a United States conquest of California, Pio Pico sold Rancho de Pala and Mission San Luis Rey to Antonio J. Cot and Jose A. Pico. The U.S. government later ruled the sale null and void.
The Franciscans abandoned all the missions except Sant Barbara and they fell into disrepair and were stripped for building material. The priests and Indians managed to keep the chapel in repair throughout the remainder of the 1800s. The chapel and west wing of the quadrangle never suffered as much deterioration as at other missions and much of the original material remains. In September 1885, Reverend Jose Mut of Mission San Juan Capistrano visited Pala and recorded the spending $214.67 for repairs to Mission Pala. William Veal received a patent to the lands and buildings of Papa Asistencia which irritated the Indians. His Catholic wife persuaded im to give the chapel, two rooms, and the cemetery to the church.
On Christmas Day in 1899, an earthquake damaged the chapel which was repaired by the local residents with help from the Landmarks Club of Southern California. The Landmarks Club acquired the remaining land and buildings and returned the mission to the Catholic Church in 1902. In 1902, Congress bought 3500 acres of land to establish a permanent reservation. In 1903, the US Government relocated the Cupeños Indians from Warner Hot Springs to Pala. The two groups worked together to restore the mission. The mission now sits on the Pala Reservation. A flood damaged the campanile (bell tower) in 1916 when the adobe base was undermined which resulted in the collapse of the structure. The tower was quickly repaired in time for the centennial of the mission's original founding.
In 1948, The Sons of the Sacred Heart, also known as Verona Fathers, also referred to as The Camboni Fathers, assumed responsibility for Mission Pala. In 1954, Father Januarius Carillo began a restoration of the quadrangle. The restoration was completed n 1959. The restoration was declared the most faithful of the California missions. In May of 1991, the Mission was returned to the Diocese of San Diego. As of June 1996 the Barnabite Fathers are in charge of the Pala Mission. Termite damage to the chapel was repaired in 1992. In 1958, the Pala Mission School began under the direction of the Sisters of the Blessed Sacrament and Sisters of the Precious Blood. Today the school is a Charter School of the Bonsall Union School District, no longer a Catholic School.
Today, the Mission continues to serve the local Indian tribes that it was intended for at it’s inception. The Holy Mass is celebrated daily. The submissions of St. Bartholomew’s on the Rincon Indian Reservation, Our Lady of Refuge on the La Jolla Indian Reservation, and St. James on the Pauma Indian Reservation continue to work through Mission San Antionio de Pala.
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