It remains a matter of conjecture whether the earliest settlers in Honduras  arrived over land from Asia via the Bering Strait, as many believe, or on rafts from the South Pacific islands. Whatever route they took, the first people to live in what is now Honduras had arrived by about 10,000 B.C.
Next to nothing is known about these early Americans. Archaeologists hypothesize the earliest of them were hunters and gatherers who may have spent only a short time in the region before continuing on to South America.
Because of its position in the center of the Americas, Honduras  was a crossroads for pre-Columbian indigenous cultures, a border zone of sorts where Mesoamerican and South American indigenous peoples met.
At some point between 3000 and 1000 B.C., the region was populated by migrants from both the north and the south. Linguistic evidence indicates that the ancestors of today’s Pech and Tawahka migrated up from South America, while the forebears of the Tolupán appear related to the Sioux of North America. Because the Lenca language as well as dozens of other idioms previously spoken in Hondura] have been lost, it’s impossible to determine where the other pre-Hispanic inhabitants came from. The earliest evidence of settled society in Honduras found thus far dates from 2000 to 1500 B.C. It appears that localized cultures developed simultaneously in the Valle de Sula, at Yarumela in the Valle de Comayagua, and in Olancho. The level of interaction between these different societies is a matter of debate, but judging from pottery remains, some intergroup trading took place. A great deal of investigation remains to be done in Honduras, where numerous ruins of unknown origin are still untouched by archaeologists. Olancho and the inland parts of the Mosquitia, in particular, are filled with ruins large and small.
Around or shortly after the time of Christ, several indigenous groups from Mexico and Guatemala migrated into Honduras . The Toltec-speaking Chorotega are thought to have first settled in western Honduras and later continued southward to the Choluteca  plain, where they were living at the time of the Spanish conquest. The Nahuatl-speaking Pipil migrated south from Mexico at about the same time.
Not long thereafter, another group moved into western Honduras from Mexico and Guatemala and set the foundations for an explosion of development. These people—who would become the Maya—went on to build one of the greatest civilizations ever known in the Americas.
An unknown people, thought to have links with the Teotihuacán culture in Mexico, crossed the Sierra Espíritu Santo from Guatemala into the valley of Copán around A.D. 100, conquering the Maya-speaking inhabitants of the region. After a slow beginning, these new rulers consolidated their local control over the next three centuries and began construction of the city of Copán by the 5th century.
The first positively dated glyph at Copán was made in A.D. 426 to mark the accession of Yax K’uk’ Mo’ to the city’s throne. Thus began the ruling dynasty of Copán, which spanned four centuries, ending sometime around A.D. 822. While Copán clearly had links to other cities in Guatemala and Mexico, it was just as often in war as in trade, in the tumultuous Mayan world of independent city-states.
For reasons not entirely clear, Copán was the greatest center for arts, astronomy, and science among the Maya. The elaborate stelae erected at Copán are unparalleled anywhere in Mesoamerica, and the city’s royal astronomers calculated planetary movements, eclipses, and the yearly calendar with a precision equaled only by modern science.
Built gradually over the course of 400 years, with old temples buried and new ones built over them, the city of Copán is an impressive testament to the wealth and vision of the Mayan rulers, and their ability to marshal large numbers of laborers. Some 24,000 people are thought to have lived in and around Copán at its height.
Mysteriously, classic Mayan civilization abruptly collapsed in the Yucatán, Guatemala, and Honduras  around A.D. 900. The collapse is all the odder considering Mayan cities were not part of one great centralized empire. One widely accepted explanation for the demise of Mayan civilization is that the population simply grew too big for the surrounding lands to support. This certainly seems to be the case at Copán, where recent studies confirm massive deforestation and soil erosion just before the city’s collapse. Although Mayan-speaking people continued to live in the Valle de Copán and still do so today, the city was abandoned entirely.
In regions outside of Mayan control, and after the decline of the Maya, Honduras was a complex mosaic of tribes, subtribes, and chiefdoms. There were only vague borders between them, and all were busy trading, bickering, and frequently warring among one another when Columbus first arrived on the scene in 1502.
Western and south-central Honduras in 1502 were dominated by the Lenca, a broad grouping composed of several different and often hostile subtribes, including the Potón, Guaquí, Cares, Chatos, Dules, Paracas, Guajiquíros, and Yaras.
The historical account of which languages were spoken by which Lenca tribes is extremely muddled. It’s possible the same groups were given two different names by different witnesses, and that others were not Lenca at all. Some tribes were exclusively hunter-gatherers, while others cultivated maize and other crops in the mountain valleys of Comayagua  and Sensetí, and around Lago de Yojoa .
In far western Honduras , the Chortí Maya held sway over the mountain region along the border with Guatemala west and south to El Salvador and were organized in local chiefdoms.
Throughout Honduras at the time of the conquest were trading outposts maintained by the Aztecs. Not far from present-day San Pedro Sula , the city of Naco—the largest urban center in the country when the Spanish conquest began—is thought to have been one such outpost, although others argue it was a Chortí Maya city.
Most of central and north-central Honduras was occupied by the Tolupán in 1502, while farther east in present-day Olancho and Mosquitia were the Pech and the Tawahka. Each of these tribes survived by hunting, fishing, and limited agriculture. Settlements were small and frequently temporary, and groups moved often to find fresh game and rich soil for planting.
Unquestionably, these various indigenous groups interacted with one another often, either through trade or warfare. In several places, they lived side by side in relative harmony, especially in the valleys of Comayagua , Catacamas, and Agalta, and around Lago de Yojoa . No group possessed the strength to exercise hegemony over the others, a fact that greatly helped Spanish invaders.