structural:expansion
Brazil

Within a few years after Cabral arrived from Brazil, competition came along from France. In 1503, an expedition under the command of Gonçalo Coelho reported French raids on the Brazilian coasts, and explorer Binot Paulmier de Gonneville traded for brazilwood after making contact in southern Brazil a year later. Expeditions sponsored by Francis I along the North American coast directly violated of the Treaty of Tordesilhas. By 1531, the French had stationed a trading post off of an island on the Brazilian coast.

The increase in brazilwood smuggling from the French led João III to press an effort to establish effective occupation of the territory. In 1531, a royal expedition led by Martim Afonso de Sousa and his brother Pero Lopes went to patrol the whole Brazilian coast, banish the French, and create some of the first colonial towns – among them São Vicente, in 1532. Sousa returned to Lisbon a year later to become governor of India and never returned to Brazil. The French attacks did cease to an extent after retaliation led to the Portuguese paying the French to stop attacking Portuguese ships throughout the Atlantic, but the attacks would continue to be a problem well into the 1560s.

Upon de Sousa's arrival and success, fifteen latitudinal tracts, theoretically to span from the coast to the Tordesillas limit, were decreed by João III on 28 September 1532. The plot of the lands formed as a hereditary captaincies (Capitanias Hereditárias) to grantees rich enough to support settlement, as had been done successfully in Madeira and Cape Verde islands. Each captain-major was to build settlements, grant allotments and administer justice, being responsible for developing and taking the costs of colonization, although not being the owner: he could transmit it to offspring, but not sell it. Twelve recipients came from Portuguese gentry who become prominent in Africa and India and senior officials of the court, such as João de Barros.

Of the fifteen original captaincies, only two, Pernambuco and São Vicente, prospered. Both were dedicated to the crop of sugar cane, and the settlers managed to maintain alliances with Native Americans. The rise of the sugar industry came about because the Crown took the easiest sources of profit (brazilwood, spices, etc.), leaving settlers to come up with new revenue sources. The establishment of the sugar cane industry demanded intensive labor that would be met with Native American and, later, African slaves. Deeming the capitanias system ineffective, João III decided to centralize the government of the colony in order to "give help and assistance" to grantees. In 1548 he created the first General Government, sending in Tomé de Sousa as first governor and selecting a capital at the Bay of All Saints, making it at the Captaincy of Bahia.

Tomé de Sousa built the capital of Brazil, Salvador, at the Bay of All Saints in 1549. Among de Sousa's 1000 man expedition were soldiers, workers, and six Jesuits led by Manuel da Nóbrega. The Jesuits would have an essential role in the colonization of Brazil, including São Vicente, and São Paulo, the latter which Nóbrega co-founded. Along with the Jesuit missions later came disease among the natives, among them plague and smallpox. Subsequently, the French would resettle in Portuguese territory at Guanabara Bay, which would be called France Antarctique. While a Portuguese ambassador was sent to Paris to report the French intrusion, Joao III appointed Mem de Sá as new Brazilian governor general, and Sá left for Brazil in 1557. By 1560, Sá and his forces had expelled the combined Huguenot, Scottish Calvinist, and slave forces from France Antarctique, but left survivors after burning their fortifications and villages. These survivors would settle Gloria Bay, Flamengo Beach, and Parapapuã with the assistance of the Tamoio natives.

The Tamoio had been allied with the French since the settlement of France Antarctique, and despite the French loss in 1560, the Tamoio were still a threat. They launched two attacks in 1561 and 1564 (the latter event was assisting the French), and were nearly successful with each. By this time period, Manuel de Nóbrega, along with fellow Jesuit José de Anchieta, took part as members of attacks on the Tamoios and as spies for their resources. From 1565 through 1567 Mem de Sá and his forces eventually destroyed France Antarctique at Guanabara Bay. He and his nephew, Estácio de Sá, then established the city of Rio de Janeiro in 1567, after Mem de Sá proclaimed the area "São Sebastião do Rio de Janeiro" in 1565. By 1575, the Tamoios had been subdued and essentially were extinct, and by 1580 the government became more of an ouvidor general rather than the ouvidores.