One of John III.'s strongest reasons for undertaking a more extensive colonisation of Brazil was the pious conviction that it was his Christian duty to promote the dissemination of the true religion in dominions which he owed to the gift of the Holy Father. He was the first and most steadfast friend of the Jesuits, then just organised and San Francisco Xavier, the Apostle of the East Indies, was sent out to one hemisphere, while the conversion of the Brazilian aborigines was determined upon in the other. With Thomas de Souza sailed an able Jesuit, Manuel Nobrega, accompanied by several other Fathers. They began a carefully planned campaign to convert the Indians and, incidentally, to exploit them in the interests of the Order.

It is impossible not to admire the courage, shrewdness, and devotion of the Jesuits. They went out alone among the savage tribes, living with them, learning their languages, preaching to them, captivating their imaginations by the pomp of religious paraphernalia and processions, baptising them, and exhorting them to abandon cannibalism and polygamy. Tireless and fearless, they plunged into an interior hitherto unpenetrated by white men. The reports they made to their superiors frequently afford the best information that is yet extant as to the customs of the Indians and the resources of the regions they explored.

The Indians were easily induced to conform to the externals of the Christian cult. Wherever the Jesuits penetrated, the aborigines soon adopted Christianity, but to hold the Indians to Christianity the Fathers were obliged to fix them to the soil. As soon as a tribe was converted, a rude church building was erected, and a Jesuit installed, who remained to teach agriculture and the arts as well as ritual and morals. His moral and intellectual superiority made him perforce an absolute ruler in miniature. Thus that strange theocracy came into being, which, starting on the Brazilian coast, spread over most of central South America. In the early part of the seventeenth century the theocratic seemed likely to become the dominant form of government south of the Amazon and east of the Andes.

The Jesuit wanted the Indian to himself, and fought against the interference or enslavement by the lay Portuguese. The colonists wanted the Indians to work on their plantations, to incorporate them as slaves, or in some analogous capacity, with the white man's industrial and civil organisation. The home government stood by the Jesuits, but the colonists constantly evaded restrictions and steadily fought the priests. The encouragement of the negro slave trade was an attempt at a compromise—intended to induce the colonists to leave the Indians alone by furnishing another supply of labour.

Primarily, at least, the Jesuit purpose was altruistic, though the material advantages and the fascination of exercising authority were soon potent motives. The Jesuits gave the South American Indian the greatest measure of peace and justice he ever enjoyed, but they reduced him to blind obedience and made him a tenant and a servant. Though virtually a slave, he was, however, little exposed to infection from the vices and diseases of civilisation; he was not put at tasks too hard for him; and under Jesuit rule he prospered. On the other hand, if this system had prevailed there would have been little white immigration, the Indian race would have remained in possession of the country, and real civilisation would never have gained a foothold.

Immediately after the founding of Bahia, Nobrega sent members of the Order to the other colonies. He himself visited Pernambuco, where the stout old proprietor met him with effective opposition. Duarte did not welcome a clergy responsible solely to a foreign corporation, and over which he could have no control. In Bahia and the south the Jesuits, however, prospered amazingly. In SÃo Paulo they laboured hard, spread widely, converted a large number of Indians, and perfected their system, but it was there they came most sharply in conflict with the spirit of individualism, and there they suffered their first and most crushing overthrow.

Thomas de Souza laboured diligently during the four years of his administration, fortifying posts, driving away contraband traders, dismissing incompetent officials, and even building jails and straightening streets where the local authorities had neglected them. He visited all the captaincies south of Bahia and entered Rio Bay, then the principal rendezvous for the French privateers and traders. He appreciated its strategic and commercial importance, and was only prevented by lack of means from establishing a strong post there. In SÃo Paulo he prohibited the flourishing trade which had grown with the Spaniards in Paraguay and Buenos Aires. Duarte da Costa, his successor, was accompanied by a large re-enforcement of Jesuits. Among them was Anchieta, one of the most notable men in the history of the Order, whose genius, devotion, and pertinacious courage laid the foundations of Jesuit power so deeply in South America that its effects remain to this day. This remarkable man was born in Teneriffe, the son of a banished nobleman, who had married a native of the island. Educated at home, from his infancy he showed marvellous talents. At fourteen, his father, not daring to risk his son's life in Spain, sent him to the Portuguese University at Coimbra. His career was so brilliant, the reputation he acquired for profound and ready intelligence, his eloquence, and his pure and elevated ideals so remarkable, that he attracted the attention of Simon Rodrigues, John III.'s great Jesuit minister, who, like all the leaders of the Order, was on the watch for talented young men. The ardent youth was easily convinced that no career was so glorious as that of a missionary, and when only twenty years old he solicited and obtained permission to go to Brazil. Nobrega, the Provincial, selected him to go to SÃo Paulo and establish a school to train neophytes and proselytes into evangelists. His own letter to Nobrega best tells what a life he found and what sort of man he was:

They herded together to keep warm, for in winter it is cold on the SÃo Paulo plateau. They had no food except the mandioc flour, fish, and game which the Indians gave them. To the little college came Creoles and half-breeds and learned Latin, Portuguese, Spanish, and Tupi. Anchieta was indefatigable. Within a year he had acquired a complete mastery of the Indian tongue, and had devised a grammar for it. He wrote his own text-books, and employed his great poetical talents in composing hymns and verses to be chanted to the pupils, recounting the stories of Holy Scripture. He visited the most savage tribes in person, and acquired a marvellous moral supremacy over them. When the Tamoyos attacked the Portuguese, and the destruction of all the southern settlements seemed inevitable, he fearlessly went to the Indian camps and persuaded the chiefs to consent to a truce while he remained among them three years as a hostage to guarantee its faithful performance by his countrymen. The savages regarded him as more than human, and tradition tells of the miracles he performed. It is related that during these three years of solitary captivity he composed, without the aid of pen or paper, his Latin "Hymn to the Virgin," celebrated as one of the masterpieces of ecclesiastical poetry.

He and his companions did not disdain to labour with their hands. They used the spade and trowel, made their own shoes, taught the Indians agriculture, introduced new plants from Europe, practised medicine, and studied the botany, topography, and geology of the country. The villages of converted Indians under their government and protection rapidly spread over the SÃo Paulo plains, and they were refuges for Indians flying from slavery on the plantations. The colonists pursued their fugitive slaves, and soon were at open war with the Jesuits. In the course of this conflict the original half-breed settlement on the plateau was destroyed and the lay Portuguese came near being wiped out. Peace was temporarily patched up, but the Paulistas soon turned the tables and compelled the Jesuits to devote themselves to their educational institutions in the towns, or to withdraw farther and farther into the wilderness.