Beginning at San Diego in 1769, Franciscan missionaries established twenty-one missions along the Alta California coast, drawing surrounding Indigenous communities into settlements organised around compulsory labour, religious instruction and residential segregation of unmarried women and girls. Once baptised, a neophyte was not free to leave: departure was treated as flight, and soldiers were sent to retrieve runaways, a practice documented in mission and presidio correspondence. Mortality was extreme — the registers record 63,789 deaths against 87,787 baptisms — driven by introduced disease, crowded dormitories, poor nutrition and high infant and maternal death rates, so that the system depended on continuous new recruitment from further inland. Resistance included the Chumash revolt of 1824. Mexican secularisation from 1833 dispersed the mission populations without restoring their land, leaving survivors as labourers on the ranchos. Historians and Native Californian communities disagree sharply over whether the missions are best described as coercive confinement or as religious congregation, a dispute that surfaced publicly around the 2015 canonisation of Junipero Serra. The atlas began its California coverage only in 1846.
Franciscan missionaries backed by Spanish and then Mexican soldiers congregated coastal Native Californians at twenty-one missions, where baptised people were not free to leave
Sherburne Cook's reconstruction from mission registers and ethnographic territory estimates puts the coastal mission zone at roughly 64,000-72,000 people in 1769, within a statewide native population he estimated at about 310,000. Later scholarship (Cook's revision, Milliken) supports a coastal figure in the same range.
The figure is the number of deaths of Indigenous neophytes recorded in the mission burial registers to 31 December 1832 — an unusually firm count, though it excludes deaths of people who fled and those in communities affected by mission-borne epidemics without entering the system. The overwhelming majority were from introduced disease, malnutrition and childbirth rather than direct killing; historians disagree over how far the conditions of confinement caused that mortality.
Mission and presidio correspondence, including the 1799 complaint of Father Antonio de la Concepcion Horra and the reports of visiting officials, document compulsory labour, the pursuit of runaways, corporal punishment and sexual violence by soldiers.
United States of America