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Portuguese navigators first discovered the islands between 1469 and 1472. The first successful settlement of Sao Tome was established in 1493 by Alvaro Caminha, who received the land as a grant from the Portuguese crown. Principe was settled in 1500 under a similar arrangement. By the mid-1500s, with the help of slave labor, the Portuguese settlers had turned the islands into Africa's foremost exporter of sugar. Sao Tome and Principe were taken over and administered by the Portuguese crown in 1522 and 1573, respectively.

Sugar cultivation declined over the next 100 years, and by the mid-1600s, Sao Tome was little more than a port of call for bunkering ships. In the early 1800s, two new cash crops, coffee and cocoa, were introduced. The rich volcanic soils proved well suited to the new cash crop industry and soon extensive plantations (roças), owned by Portuguese companies or absentee landlords, occupied almost all of the good farmland. By 1908, Sao Tome had become the world's largest producer of cocoa, still the country's most important crop.

The roças system, which gave the plantation managers a high degree of authority, led to abuses against the African farm workers. Although Portugal officially abolished slavery in 1876, the practice of forced paid labor continued. In the early 1900s, an internationally publicized controversy arose over charges that Angolan contract workers were being subjected to forced labor and unsatisfactory working conditions. Sporadic labor unrest and dissatisfaction continued well into the 20th century, culminating in an outbreak of riots in 1953 in which several hundred African laborers were killed in a clash with their Portuguese rulers. This "Batepa Massacre" remains a major event in the colonial history of the islands, and the government officially observes its anniversary.