The first inhabitants of the region that is now Equatorial Guinea are believed to have been Pygmies, of whom only isolated pockets remain in northern Rio Muni. Bantu migrations between the 17th and 19th centuries brought the coastal tribes and later the Fang. Elements of the latter may have generated the Bubi, who immigrated to Bioko from Cameroon and Rio Muni in several waves and succeeded former Neolithic populations. The Annobon population, native to Angola, was introduced by the Portuguese via Sao Tome.

The Portuguese explorer, Fernando Po (Fernao do Poo), seeking a route to India, is credited with having discovered the island of Bioko in 1471. He called it Formosa ("pretty flower"), but it quickly took on the name of its European discoverer. The Portuguese retained control until 1778, when the island, adjacent islets, and commercial rights to the mainland between the Niger and Ogoue Rivers were ceded to Spain in exchange for territory in South America (Treaty of Pardo). From 1827 to 1843, Britain established a base on the island to combat the slave trade. Conflicting claims to the mainland were settled in 1900 by the Treaty of Paris, and periodically, the mainland territories were united administratively under Spanish rule.

Spain lacked the wealth and the interest to develop an extensive economic infrastructure in what was commonly known as Spanish Guinea during the first half of this century. However, through a paternalistic system, particularly on Bioko Island, Spain developed large cacao plantations for which thousands of Nigerian workers were imported as laborers. At independence in 1968, largely as a result of this system, Equatorial Guinea had one of the highest per capita incomes in Africa. The Spanish also helped Equatorial Guinea achieve one of the continent's highest literacy rates and developed a good network of health care facilities.

In 1959, the Spanish territory of the Gulf of Guinea was established with status similar to the provinces of metropolitan Spain. As the Spanish Equatorial Region, it was ruled by a governor general exercising military and civilian powers. The first local elections were held in 1959, and the first Equatoguinean representatives were seated in the Spanish parliament. Under the Basic Law of December 1963, limited autonomy was authorized under a joint legislative body for the territory's two provinces. The name of the country was changed to Equatorial Guinea. Although Spain's commissioner general had extensive powers, the Equatorial Guinean General Assembly had considerable initiative in formulating laws and regulations.

In March 1968, under pressure from Equatoguinean nationalists and the United Nations, Spain announced that it would grant independence to Equatorial Guinea. A constitutional convention produced an electoral law and draft constitution. In the presence of a UN observer team, a referendum was held on August 11, 1968, and 63% of the electorate voted in favor of the constitution, which provided for a government with a General Assembly and a Supreme Court with judges appointed by the president.

In September 1968, Francisco Macias Nguema was elected first president of Equatorial Guinea, and independence was granted in October. In July 1970, Macias created a single-party state and by May 1971, key portions of the constitution were abrogated. In 1972 Macias took complete control of the government and assumed the title of President-for-Life. The Macias regime was characterized by abandonment of all government functions except internal security, which was accomplished by terror; this led to the death or exile of up to one-third of the country's population. Due to pilferage, ignorance, and neglect, the country's infrastructure--electrical, water, road, transportation, and health--fell into ruin. Religion was repressed, and education ceased. The private and public sectors of the economy were devastated. Nigerian contract laborers on Bioko, estimated to have been 60,000, left en masse in early 1976. The economy collapsed, and skilled citizens and foreigners left.

In August 1979, Macias' nephew from Mongomo and former director of the infamous Black Beach prison, Teodoro Obiang Nguema Mbasogo, led a successful coup d'etat; Macias was arrested, tried, and executed. Obiang assumed the Presidency in October 1979. Obiang initially ruled Equatorial Guinea with the assistance of a Supreme Military Council. A new constitution, drafted in 1982 with the help of the United Nations Commission on Human Rights, came into effect after a popular vote on August 15, 1982; the Council was abolished, and Obiang remained in the presidency for a 7-year term. He was reelected in 1989. In February 1996, he again won reelection with 98% of the vote; several opponents withdrew from the race, however, and the election was criticized by international observers. Subsequently, Obiang named a new cabinet, which included some opposition figures in minor portfolios.

Despite the formal ending of one-party rule in 1991, President Obiang and a circle of advisors (drawn largely from his own family and ethnic group) maintain real authority. The President names and dismisses cabinet members and judges, ratifies treaties, leads the armed forces, and has considerable authority in other areas. He appoints the governors of Equatorial Guinea's six provinces. The opposition had few electoral successes in the 1990s. By the early 21th century, President Obiang’s PDGE party fully dominated government at all levels.