To secure Las Californias, which were largely unsettled, the Spanish government colonized the land with religious (misiónes), civilian (pueblos) and military (presidios) posts. On the religious front, Spain sponsored Jesuits to build missions in Baja California and Christianize the indigenous people. Their initial efforts had limited success. But with the threat of Russian encroachment in Alta California, Spain shifted focus and authorized establishment of missions throughout Alta California under Franciscan Junipero Serra, who was appointed as the first Father-Presidente: the leader of all Catholic missions in Alta and Baja California. Franciscan missions, asistencias (sub-missions) and estancias (ranches supporting the missions) sprung up from 1769 - 1823 throughout Alta California. (In Baja California, the Jesuit equivalent of an asistencia is a visita.)
Franciscans built just 1 mission in Baja California, though Dominicans went on to build 11 more there. Misión Loreto, the second mission in Las Californias, remained the headquarters of Las Californias' mission system until 1829. The Catholic orders required the permission of the Spanish government to create new establishments, whether missions, asistencias (sub-missions) or estancias (ranch outposts that supported the missions). Spain also set up presidios (military forts to protect the surrounding regions) and pueblos (civilian towns) as part of their strategy to exert hegemony. Alta California was divided into four military districts, each with its own presidio. There was tension between the military and religious spheres.
Sonora y Sinaloa
In 1598, Don Juan de Oñate entered the Southwest with 500 people and claimed for Spain some of the Pueblo Indians' land. He began to establish a colony and granted encomiendas (the right to force Indian labor) to favored Spaniards. In 1609, Spaniards founded Santa Fe. The colony's economy centered on cattle and sheep raised on the vast ranchos.
Despite widespread conversions to Catholicism, most natives (including the converts) continued to practice their own religious rituals. In 1680, Spanish priests and the colonial government tried to suppress these rituals. In response, Pope, an Indian religious leader, led an uprising that killed hundreds of European settlers, captured Santa Fe, and drove the Spanish from the region. Twelve years later, the Spanish returned and crushed a last revolt in 1696. Brinkley, p 12
The Pueblo Indian population was decimated while the Spanish population grew. However, the Spanish were still outnumbered all way into the later 18th century.