Bioko was claimed by (and until 1972 named after) Fernão do Po, a Portuguese navigator, in 1472, and Annobón was also claimed. During the 17th cent. the mainland's indigenous pygmy peoples were displaced by other groups, principally the Fang, who now inhabit the area. In 1778, Portugal ceded the islands, and also the commercial rights to a part of the African coast that included present-day Río Muni, to the Spanish. Hoping to export Africans as slaves to their American possessions, the Spanish sent settlers to the islands, but they died of yellow fever, and by 1781 the region was abandoned by the Europeans.

From 1827 to 1843 the British leased bases at Malabo (then called Port Clarence) and San Carlos from Spain for use by their antislavery patrols, and some freed slaves were settled on Bioko (then called Fernando Po). In 1844 the Spanish reacquired Bioko and began to occupy it. In 1879, a Cuban penal settlement was established there, and some of the convicts remained on the island after being released from prison. The general region of Río Muni was awarded to Spain at the Conference of Berlin in 1885, and its boundaries were defined precisely in a treaty with France in 1900. The islands and Río Muni were grouped together as the colony of Spanish Guinea.

Under the Spanish, economic development was largely confined to Bioko, although some measures were taken in Río Muni beginning in the 1940s. By 1960, about 6,000 Europeans (mostly Spanish) were living in the colony, and they controlled the production of cocoa and timber. In 1959 the colony was reorganized into two overseas provinces of Spain, each under a governor. In a further move to assimilate the region to Spain, three Hispano-Guineans were elected to the Spanish Cortes in 1960. However, nationalists were not satisfied with assimilation and demanded independence.

In 1963, Spain granted the country (renamed Equatorial Guinea) a limited amount of autonomy, and on Oct. 12, 1968, it received complete independence. The first president was Francisco Macías Nguema, a Fang from Río Muni. In 1969, there were violent anti-European demonstrations in Río Muni and most Europeans left the country, thus for a time severely dislocating the economy. In 1970 all political parties were merged into the United National party (PUN), headed by Macías Nguema, who in 1972 was appointed president for life. In 1973 a new constitution was adopted that abolished the nation's two semiautonomous provinces and created a unitary state.

Macías Nguema led a dictatorship characterized by campaigns against intellectuals and all those alleged to be plotting the overthrow of the regime; many were imprisoned, killed, or driven into exile. Nigerian migrant workers demanding higher wages were brutally suppressed, straining relations between Nigeria and Equatorial Guinea. Relations with Cameroon and Gabon were also strained as refugees fled to those countries. Equatorial Guinea severed its diplomatic ties with Spain in 1977. Spanish plantation owners shut down their operations, foreign investment declined, and the nation suffered a severe drop in population, with some 25,000 to 80,000 of the country's inhabitants estimated to have been killed by the government.

In 1979 the military staged a coup, executing Macías Nguema and installing his nephew, Lt. Col. Teodoro Obiang Nguema Mbasogo, as head of the military and head of state. Obiang Nguema Mbasogo lifted restrictions on the Roman Catholic Church, freed political prisoners, encouraged refugees to return, and restored diplomatic ties with Western nations. Spain and France began to reinvest, and the European Community helped rehabilitate the road system. These efforts met with limited success.

In 1982 a new constitution was approved that called for a more democratic political structure, and a decade later legislation was passed providing for a multiparty democracy. However, by 1993, when legislative elections were held, only one party, Obiang Nguema Mbasogo's Democratic Party for Equatorial Guinea (PDGE), held significant power, and the regime was widely denounced for its continued repression of opposition groups. In the 1996 multiparty presidential elections, which were boycotted by major opposition parties, the president won a landslide victory. In the late 1990s, over 100,000 citizens lived in exile abroad, and there was wide dissatisfaction with the slow pace of reform.

Obiang Nguema Mbasogo was reelected unopposed in 2002 after opposition candidates, expecting fraud, withdrew. In Mar., 2004, the government foiled an apparent coup attempt involving mainly South African mercenaries. The national legislative elections two months later occurred in a climate of intimidation that assured a new total victory for the PDGE and its allies. When police blamed Cameroonians for armed robberies in late 2007, hundreds of Cameroonians faced harassment in Equatorial Guinea; Equatorial Guineans in Cameroon were similarly harassed in revenge.