San Jose del Cabo History, as with many others, is one of natural native riches and forced conquest of land. Baja California Sur was originally home to Pericu, Guaycura and Monqui native Indians. There are several dozen Pericu skulls kept by the Regional Museum of La Paz in Baja California Sur in Mexico and the National Museum of Anthropology and History in Mexico City that suggest they were relatives to other populations of the Pacific and Indian Ocean areas. Pericu-Guaycura-Monqui group consisted of around an estimate of 4,000 persons in 1734 and 400 in 1772–a reduction that implies that they lived isolated from the outside world for a long time before the Spanish missionaries arrived in in the 17th century.
The Pericu indians called San Jose del Cabo Añuití. Their division of labor was based primarily on sex and age and they were monogamous and polygamous. Local communities were independent of each other and there was no superior authority. Leadership positions within local communities tended to be hereditary and went mostly to males, but occasionally positions of leadership were also held by women. They are not known for being entirely peaceful communities at one with nature and the environment; they were in constant conflict over territory and hunting rights with the other native tribes.
Spanish galleons first visited Estero San Jose at the mouth of the Rio San Jose to obtain fresh water near the end of their voyages from the Philippines to Acapulco in the late 17th and early 18th centuries. In their attempts to impose new beliefs and take possession of the land and local culture, the Spanish founded their missions along the Baja.
In 1730, Jesuit Padre Nicholas Tamaral traveled south from Mission La Purisima and founded Mission San Jose del Cabo on a mesa overlooking the Rio San Jose, some 5 kilometers north of the current town site, but the overwhelming presence of mosquitoes forced them to move to the mouth of the estuary on a rise flanked by Cerro del Vigia and Cerro de la Cruz. Tamaral was killed in October of 1734, when the indians burned both the San Jose and Santiago missions in a rebellion.
A presidio was established by the Spanish shortly thereafter to protect themselves from insurgent Indians and protect the estuary from English pirates. By 1767, virtually all the Indians in the area had died either of European diseases or in battle with the Spanish. San Jose del Cabo remained an important Spanish military outpost until the mid-19th century when the presidio was turned over to Mexican nationals.
Its population was lost after the mining in the region gave out in the late 19th and 20th centuries. In 1940, the Church was rebuilt, and San Jose del Cabo began attracting sportfishers and celebrities in the ’60s and ’70s, but not much has changed the Spanish colonial character of the town. Its 18th century architecture preserves its relaxed ambiance that invites artists, musicians and yogis alike to live together. Nowadays, creative and productive people call San Jose del Cabo home.