Though Trujillo was officially founded on May 18, 1525, by Juan de Medina, acting under orders from Hernán Cortés, the natural bay had long before drawn other settlers. According to colonial testimony and archaeological evidence, Trujillo Bay had been occupied for many hundreds of years before the Spanish arrived. Trujillo was apparently something of a pre-Columbian crossroads, the site of Pech and Tolupán villages as well as settlements of Mayan and Nahuatl traders from Mexico and Guatemala.

The early Spanish colonists established their new town on the site of an Indian village named Guaimura, amid approximately a dozen other villages totaling several thousand inhabitants. Trujillo was named for the Spanish hometown of Medina’s superior officer, Fernando de las Casas.

In the first years after conquest, Trujillo was the administrative center of the new colony, housing both the governor of Honduras and the only bishopric, established in 1545. But the lure of gold in the mountains soon drew colonists to the interior towns of Gracias a Dios and Comayagua, which by the middle of the century had superseded Trujillo.

Trujillo faded into a backwater colonial port. The constant threat of pirate assault on the poorly guarded harbor was all the more reason for colonists to relocate. French corsairs first attacked in 1558, and others followed repeatedly from their bases on the Bay Islands and in the Mosquitia. Since colonial authorities were unable to mount an effective defense, even the Spanish merchants who depended on the port took to living inland and came to the coast only when the Spanish fleet arrived.

In 1642, English pirate William Jackson led an assault on Trujillo with 1,500 men, almost entirely destroying the town. While Trujillo residents were still recovering from the blow, the next year Dutchman Jan Van Horn arrived and finished the work entirely. Those who hadn’t been killed gave up the port as a lost cause, and the Spanish deserted Trujillo for almost 150 years, although British traders intermittently used the ruined town as a stop-off point.

In the late 18th century, the Spanish began a major counteroffensive to turn back British settlements along Central America’s Caribbean coast. As part of this effort, Trujillo was reoccupied by a contingent of soldiers in 1780. Although the Spanish colony was on its last legs, the new settlement took hold. It received a boost in 1799, when several hundred Garífuna, deported by the British from the south Caribbean island of San Vicente and unceremoniously dumped on nearby Roatán, built a village just west of Trujillo in what is now Barrio Cristales.

As with the rest of the north coast, Trujillo participated in the banana boom of the early 20th century. Both Standard and United Fruit acquired lands in the area. Standard still controls much land in the nearby Valle del Aguán and ships most of its produce out of nearby Puerto Castilla. Trujillo’s economy relies on the port, the departmental government, and the fledgling tourist industry.