Indigenous peoples were severely impacted by the introduction of European diseases such as smallpox and measles; furthermore, the expulsion of the Jesuits from the Spanish Empire in 1767 ripped the social fabric of the peninsula, although Franciscans were sent to replace them.
In addition to the presidio (royal fort) and pueblo (town), the misión was one of three major agencies employed by the Spanish crown to extend its borders and consolidate its colonial territories.
Asistencias ("sub-missions" or "contributing chapels") were small-scale missions that regularly conducted Catholic religious services on days of obligation, but lacked a resident priest.
In 1696, the Pious Fund for the Californias was founded at Jesuit headquarters in Mexico City, the idea being that this endowment could produce enough revenue every year to give the critical financial support to a second missionary effort, which was undertaken by Juan Maria Salvatierra in 1697 starting with Mission Loreto.
Ignacio Tirsch, a Jesuit friar of the 1760s, drew a picture of such a Manila galleon trading at Mission San Jose del Cabo.
Once empowered to erect a mission in a given area, the men assigned to it chose a specific site that featured a good water supply, proximity to a population of indigenous peoples, and arable land.
The padres, their military escort and often converted mainland indigenous people or mestizos initially fashioned defendable shelters, from which a base was established and the mission could grow.
The workshops, kitchens, living quarters, storerooms, and other ancillary chambers were usually grouped in the form of a quadrangle, inside which religious celebrations and other events often took place.
[5] The Kumeyaay and Cocapah practiced limited agriculture, but the majority of the Baja Californians were nomadic or semi-nomadic hunter-gatherers who eked out a living under difficult desert conditions and scarcity of fresh water.
In a policy followed throughout much of Latin America called reductions, the missionaries concentrated the Indians at or near the mission for religious instruction and training to become sedentary farmers and stock herders.
Their goal was to create a self-sufficient theocracy in which the missionary, usually supported by Spanish soldiers and laymen, attempted to rule over every facet of the Indian's religious and secular lives.
In January 1683, the Spanish government chartered an expedition consisting of three ships to transport a contingent of 200 men to the southern tip of Baja California.
Under the command of the governor of Sinaloa, Isidoro de Atondo y Antillón, and accompanied by Jesuit priest Eusebio Francisco Kino, the ships made landfall in La Paz.
The missionaries attempted to establish a settlement near present-day Loreto, which they named Misión San Bruno but failed for lack of supplies.
Fifteen priests and one lay brother survived the hardships, only to be subjected to enforcement of the decree launched against the Society by King Carlos III of Spain.
Gaspar de Portolà was appointed Governor of Las Californias, with orders to supervise the Jesuit expulsion and oversee the installation of replacement Franciscan priests.
In 1810, Mexico sought to end Spanish colonial rule, gaining her independence in 1821, after which Mexican President Guadalupe Victoria named Lt. Col. José María Echeandía governor of Baja California Sur and divided it into four separate municipios (municipalities).