Bahia was discovered in the period when the commerce with the Indic ports was quite compensating for Portugal. Therefore, the Portuguese kingdom had no reasons to dedicate much attention to its new colony. Only after going through a serious financial crisis and becoming aware of the incursions of the French in the Brazilian seashore, the Portuguese felt the need to claim the new land. Following advice, Dom João III decided to divide the colony, donating land under the form of hereditary captaincies. Five were donated in Bahia’s territory: All Saints’ Bay Captaincy to Francisco Pereira Coutinho; Porto Seguro to Pero de Campos Tourinho; Ilhéus to Jorge de Figueiredo Correia; Itaparica to Dom Antonio de Athaíde and Recôncavo to Álvaro da Costa.
With the need to create a political and administrative center able to congregate all the captaincies, a general government was instituted in 1549. The first general governor, Tomé de Souza arrived in Salvador on March 29th. Besides settlers and employees of the Crown, Tomé de Souza conducted the six first Jesuits led by the priest Manoel da Nobrega. Soon afterwards the first diocese of the colony was created, led by Dom Pero Fernandes Sardinha.
In 1553, Duarte da Costa arrived to substitute Tomé de Souza. He brought with him more Jesuits , among them José de Anchieta. Mem de Sá substituted Duarte da Costa. His government was marked by the harmony with the Church. Until the Dutch invasion, 12 more Portuguese governed Brazil, whose capital was Bahia.