They were named by the founding missionaries in honor of a saint. As Donald Toomey, in his marvelous book The Spell of California’s Spanish Colonial Missions has pointed out, the act of naming “allowed the community settling there to Hispanicize and Christianize” the wilderness. The name chosen inserted the mission into the liturgical calendar. Each mission held a fiesta on the Saints day.
Each name has a story. The first mission was named San Diego de Alcala because this was the name given to the bay of San Diego by Captain Sebastian Vizcaino when he explored the coast in 1602. The name San Diego was applied to both the presidio and the mission when they were founded in 1769. San Carlos Borromeo de Carmelo was chosen as the patron for the second mission as a gesture to honor King Carlos III of Spain. Saint Charles Borromeo was a 16th century Italian Cardinal. He was canonized in 1610. Fr. Junipero Serra chose the name for the third mission, San Antonio de Padua, a Franciscan who was canonized in 1231, the year following his death.