The official history of Morro de São Paulo begins in 1531, Martim Afonso de Souza - a portuguese navigator discovers the island and names it 'Tynharéa' which later becomes Tinharé.
In 1534 the territory which today is the state of Bahia was divided into three Hereditary Captainships which were extensions of foi dividido em três Capitanias Hereditárias, being extensions of territory donated by the king of Portugal to close trustees for colonization.
These Captainships were: Porto Seguro, Bahia and Ilhéus which comprised Costa do Dendê where the island Tinharé is located.
The Captainships Ilhéus, was entrusted to Jorge de Figueiredo Correa, who chose to stay in Portugal and sent Francisco Romeiro as his representative to colonize the territory. In 1535, Francisco Romeiro arrived on the island of Tinharé and founded the village Morro de São Paulo in the very north of the island.
After several years Morro de São Paulo assumed an important role of defense of the Brazilian coast, which already was under permanent attack of various forign forces at that time.
In 1624, the Dutch comandander Johan Van Dortt landed in Tinharé antes with his forces to attack the city of Salvador. In order to protect the archipel and the strategic passage to Salavador for being used for attacs the construction of the fortress of Morro de São Paulo started in 1630 under the command of governor Diogo Luiz de Oliveira.
After more than a century of construction in 1748 the fortress was surrounded by a lrage wall streching almost 1000 meters in length with 183 soldiers and 51 pieces of artillery.
In 1746 the so called 'Fonte Grande' was build - a site for water treatment was built so the soldiers at the fortress and the inhabitants of the village could be supplied with drinking water. Between 1850 and 1855 the lighthouse (farol) was built by the enrineer João Monteiro Carson to help navigators of vessels.
In 1859 Morro de São Paulo was visited by the Brazilian royal family and D. Pedro II. According to his notes the village was inhabited by approximately 300 familes.
In the late colocial period Morro de São Paulo lost lots of its military importance and turned into a quiet village for fishermen. Only in the beginning of the 60s' tourism started to develop in Morro de São Paulo - in the beginning mainly summer tourists from Salvador. In the next decade more and more hippies began settling on the island which contributed to the image the island is has today worldwide.