The indigenous people of Honduras are believed to have migrated to Central America more than 10,000 years ago. The Mayan civilization, an advanced culture that flourished in Central America for hundreds of years before the Europeans arrived, included present-day Honduras. The ancient Mayan city of Copán (in what is now western Honduras) was a centre for art, mathematics and astronomical studies. People from the Caribbean also settled in Honduras.

In 1502, Christopher Columbus landed in Honduras, but he did not establish a settlement. In the 1520s, several Spanish military leaders in Central America tried to establish supremacy in the area. They fought with each other and with the indigenous people over the land. In 1524, Hernán Cortés, the Spanish conquistador who ruled much of Mexico, came to Honduras to impose order. He established some Spanish settlements, but fighting resumed when he left two years later.

The Spanish colonists, who were mining for gold and silver, building plantations and establishing churches, forced the indigenous people to provide labour. Many died from disease and mistreatment. In 1537, an uprising of indigenous people was led by Lempira, a Lenca chief. After two years of war, the Spanish called for peace talks. Lempira agreed to negotiate, but the Spanish murdered him and then defeated the indigenous army.

By the 17th century, the gold and silver mines were depleted, and Spain lost interest in the colony. Some English people settled on the Bay Islands during this time. Central America declared its independence from Spain in 1821. Honduras joined the United Provinces of Central America with Nicaragua, El Salvador, Costa Rica and Guatemala. In 1838, it declared its independence from the federation of provinces.

In the late 19th century, American enterprises, notably Standard Fruit and United Fruit, bought land in Honduras to grow bananas. Honduras became dependent on the banana industry, which was controlled by American companies. These companies acquired great power in Honduras. Throughout much of the 20th century, the U.S. military used Honduras as a military base for some of its operations against other Central American countries.

In 1969, war broke out between Honduras and El Salvador. The Guerra de Fútbol or Soccer War began when Salvadorans attacked Honduran fans at a soccer game and escalated until El Salvador bombed Honduran airports. Although the war lasted only 100 hours, a peace treaty was not signed until 1980. The original territorial dispute was resolved by the World Court in 1992.

The 1990s were a time of high inflation and increasing poverty in Honduras. Hurricanes and floods added to the country's economic difficulties. The president of Honduras since 1998 has been Carlos Roberto Flores Facussé.

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In 1830, Francisco Morazán, a Honduran military leader, was elected president of the United Provinces of Central America. He worked to improve education, the justice system and regional economic development. Many streets, parks and towns in Honduras are named after Morazán, who is considered the father of Central America.