San Diego de Alcalá, the first of the twenty-one great California Missions, marks the birthplace of Christianity in the west coast of the United States. It is California's first Mission Church. This remarkable and significant historical shrine provides an understanding and appreciation of the beginning of Catholicism in this corner of the world, so remote from the Mother Country of Spain and yet so similar.

Today the Mission, which was founded in 1769, serves as an active parish church and cultural center for people of all faiths who are welcome to visit and relive the grandeur and excitement of more than two centuries of California history and tradition.

For thousands of years, the American Indians lived in this area that we now know as the great state of California. Most of the maps before the 18th century depicted California as an island. In 1542, Juan Rodríguez Cabrillo, an explorer commissioned by the monarch of Spain, arrived in San Diego Bay, and according to the Spanish tradition named it San Miguel, after the saint whose feast day was closest to the landing. In 1602 Sebastian Viscaino, leading another Spanish expedition, entered the harbor and renamed it San Diego after Saint Didacus of Alcalá, who died in Alcalá de Henares, Spain, on November 12, 1463, and whose feast day was closest to the landing. San Diego, who was born in 1400 in San Nicolás del Puerto, Spain, was also the name of the flagship for this expedition.

Real and perceived incursions by Russian or other foreign powers into the Spanish territory of Alta California, prompted the King of Spain, Carlos III, to issue instructions to the Governor of Baja California, Gaspar de Portolá, concerning the vigilance and protection of this territory of the New Spain. To Inspector-General Don José de Gálvez and other high-ranking officials the experience of two centuries in Baja California had demonstrated that, while soldiers might defend the country against foreign enemies, they could not transform the indigenous people of Alta California into loyal subjects. The Californias were the most unattractive territory to the ambitious, success-seeking colonists of the New Spain. Galvez therefore procured the experience, ingenuity, and religious zeal of Saint Junipero Serra and the Franciscan Padres, to undertake the conversion to Christianity of all the Indians living in Alta California, and to secure these converts as loyal subjects of the Spanish Crown.

The Franciscan Friars who were assigned to the Baja California missions were chosen to establish the missions in Alta California. The military, who accompanied the Friars, would protect and support them. Father Junipero Serra was chosen Superior of the Franciscan missionaries and Gaspar de Portolá, Governor of Baja California, was designated the leader in charge of the expeditions.

Five expeditions were dispatched from New Spain (Mexico) - three ships, the San Carlos, the San Antonio and the San Jose and two land expeditions. The San Carlos and the San Antonio set sail in January and February of 1769. After rough seas and many hardships, they anchored in San Diego Bay in April. The supply ship, the San Jose, which left New Spain in June, was lost at sea. Departing Baja California during March 1769, the land expeditions were slightly more successful in terms of casualties but just as difficult, leading mules and horses and carrying food, farming tools and seeds. The total casualties of the expeditions were high. According to a letter written by Father Serra and dated July 3, 1769, "The San Carlos is without sailors, for all have died of scurvy, save one and a cook."  Scurvy was raging throughout the contingent. Of the 219 who comprised the first four expeditions, slightly more than half survived.

Father Junípero Serra accompanied the second land expedition, which arrived in San Diego on July 1, 1769. Father Serra, a native Majorcan, was nearly 56 years of age. He was a small man, 5' 2" and 120 pounds and was afflicted with a chronic leg infection that caused him to limp.

On July 16, 1769, Father Serra established Mission San Diego and the California mission system was begun on a site overlooking the bay. The mission remained at this site for only five years; the water supply was not reliably sufficient to sustain the crops.  The soil was not fertile enough and the American Indians were intimidated by the military. The decision to move the mission six miles east was made by the pastor, Father Luis Jayme (a young Majorcan) and approved by Father President Serra. The new site was close to the San Diego River and the Kumeyaay village of Nipaguay.  Father Francisco Palou, in his Historical Memoirs of New California states, "The days while we were detained at the mission of San Diego (about September 1773), we went to examine some places in search of a site suitable for planting. For this purpose we examined the banks of the river in the same valley of San Diego, about two leagues from the mission (the Presidio Hill), although there was danger that the flood would carry the crops away, for they told us that in that place the rains begin early and last longer than at the mission. On the other hand, in case the rains should be short, it would be possible, with some trouble, to dam up the water of the river. This decided, the fathers at once set a hand to preparing the ground at that place, which is named Nuestra Senora del Pilar."  From 1769 to 1774, only 116 Indians had been baptized. Father Jayme and the other Franciscan Missionaries had great rapport with the Kumeyaay, baptizing 315 Indians during the summer of 1775. Unfortunately, two of the mission or Diegueno Indians became dissatisfied with the regulations and conditions established by the Spanish authorities, and they incited hundreds of Indians in remote villages to riot. According to Father Francisco Palou's report of the incidence, eight hundred American Indians stormed onto the grounds about midnight on November 4, 1775. They pillaged the mission, burned it to the ground and massacred a blacksmith, a carpenter (mortally wounded), and Father Jayme, who became California's first Catholic Martyr. He is buried next to the altar in the present church.  Survivors of the night long attack were one corporal and three Leather Jacket soldiers, one blacksmith, two children who were the son and nephew of the Presidio commandant, and Associate Pastor Father Vicente Fuster.

In 1776, Father Serra returned to Mission San Diego de Alcalá to oversee the rebuilding of the mission. Fearing there would be further attacks, the padres rebuilt the mission within a 150 feet quadrangle, with adobe walls 9 feet in height, including 3 or 4 defensive structures of a military type, called ravelins. Reestablishing the mission was a long, difficult process. This mission was always one of the poorest. The land was difficult to till, the water scarce. Slowly, Mission San Diego de Alcalá became more productive.  According to the Mission San Diego Accounts Book, from 1778 to 1795 Mission San Diego became known as an efficient horse and mule breeding farm, providing other missions in Alta and Baja California an average of 16 animals per year. San Diego would in turn receive farm products from the surplus of successful grain producing missions.  According to Franciscan historian Father Zephyrin Engelhardt, O.F.M., 1797 was our most successful year in spiritual results when 567 baptisms were performed, and neophytes numbered 908. The mission land area encompassed about 55,000 acres, harvesting corn, wheat, barley, kidney beans and chick peas; vineyards produced enough grapes for wine and gardens yielded vegetables.Sometime after 1803, following a two-year drought, the mission Padres and Diegueno Indians built a dam across the San Diego River bed, about 224 feet long, 13 feet wide, and 12 feet high, approximately five miles east of the mission. From the dam, an aqueduct was constructed. It consisted of tiles, resting on cobblestones in cement, and carried by gravity flow a stream one foot deep and two feet wide to mission lands. It was built through the north side of a dangerously steep gorge, impassable on horseback.  The 1814 mission year-end report stated that about 3 1/2 miles of the aqueduct had been completed. It is believed that by 1817 the work was completed. By 1825 the mission owned 19,420 sheep, 184 goats, 8,120 cattle, 565 horses and 115 mules. These are amazing achievements considering that the area was arid chaparral with no livestock or large scale farming until the Spanish arrived.

The olive in California was first cultivated at Mission San Diego.  None of the Padres' entries into the Mission San Diego Accounts Book, Harvest section mentioned olives, at all during the years 1777 to 1782.  Franciscan historian Fr. Zephyrin Englehardt believed that the olive came to the mission after Fr. Fermin Francisco de Lasuen succeeded Fr. Serra as Father Presidente in 1784.  In his (missions) Biennial Report for the Years 1801-1802, Fr. Lasuen states: "In some of those (missions) mentioned a beginning has been made in cultivating the olive, and in San Diego a little olive oil of good quality has already been obtained.  Eventually trees from San Diego furnished cuttings used to start olive orchards at other California missions.  Four years after the 1834 Decree of Confiscation, a Mexican government report described two olive orchards at Mission San Diego, one of 300 trees and another of 167 trees.  In 1852 John Russell Bartlett, U.S. Boundary Commissioner wrote about Mission San Diego: "The place is celebrated also for a flourishing orchard of olive trees, which still remain yielding a great abundance of olives, the excellence of which we had an opportunity of tasting on our homeward journey."  A map of the lands granted to Mission San Diego by President Abraham Lincoln on 05/23/1862, and prepared on 02/18/1860 by Deputy Surveyor Henry Hancock, included an "olive orchard" located southwest of the Mission Church.  Mission San Diego olive trees were the source of cuttings used to produce new trees for the California olive planning boom of 1868.

In 1821, Mexico gained its independence from Spain and the Mexican government did not have the same allegiance to the missions. The Act for the  Secularization of the Missions of California in 1833 and the Decree of Confiscation of 1834 removed the administration of the mission from the Franciscans and gave it to Mexican government administrators.  On April 27, 1840, at the request of the Mexican government, Pope Gregory XVI withdrew Alta and Baja California from the jurisdiction of the Diocese of Sonora, appointing Francisco Garcia Diego y Moreno, a native Mexican Franciscan, as the first Bishop of the Californias, with the see at Mission San Diego de Alcalá. Subsequent to his consecration on October 4, 1840, at the Franciscan Church of Zacatecas, Mexico, Bishop Diego landed at San Diego on December 11, 1841. Owing to the poverty and insignificance of the place, with the assistance of San Diego merchant and cargo ship owner Don Jose Antonio Aguirre on January 11, 1842, Bishop Diego removed his residence to Mission Santa Barbara. In 1846, Governor Pio Pico sold the lands of Mission San Diego de Alcalá to prominent Californio Santiago Arguello.

In 1848, after the Mexican American War, the United States Army occupied the mission grounds until 1858. The Army made numerous modifications on the mission grounds, including the conversion of the church into a two-story building, and the establishment of a military cemetery. On May 23, 1862, President Abraham Lincoln signed a proclamation returning to the Catholic Church approximately 22 acres of land, formerly utilized by Mission San Diego de Alcalá and the Dieguenos. Following the Army occupation, the mission fell into ruin, and remained abandoned until 1891 when Father Antonio Dominic Ubach and the Sisters of Saint Joseph of Carondelet moved the Saint Anthony's Industrial School for Indian children from Old Town San Diego to the mission grounds. The school at the mission closed in 1907 and was moved to Banning, California. Two dormitories were built for the students of Saint Anthony's, one of which exists today as the Religious Education Center of Mission San Diego de Alcalá.

After detailed historical research, in 1931 the Mission was rebuilt to what architects J. E. Loveless and J. Marshall Miller determined was what the 1813 church must have looked. Today it is an active Catholic parish of the Roman Catholic Diocese of San Diego, and every year is visited by thousands of fourth graders from throughout the state studying California history.