Repeated pirate raids on coastal towns along the Caribbean coast of Central America led the Spanish Crown as early as 1590 to begin looking for a new defensible port for the Captaincy General of Guatemala to export its goods to Spain.

The then-governor of Honduras, Pantaleón Ibánez, described that the town they planned would include a hospital, a building for the royal treasury, a church, warehouses, barracks for soldiers, and houses for the officers.

The town itself was to house the people who would build and occupy the two Spanish forts (El Real, and San Fernando de Omoa) which would guard the bay.

This historic place had as its main purpose to protect against the pirates that targeted the silver cargos originating from the mines of San Miguel of Tegucigalpa that often left from Omoa to Spain.

[4][failed verification] A naval packet ship (paquebote) mounting 18 guns was built here for the Spanish Navy in 1757 that also carried the name San Fernando.

They found two Spanish ships which took shelter under the guns of the fortress of San Fernando de Omoa, and an unsuccessful attempt was made to capture the town from the sea.

On 16 October, this was followed by a landing some 9 miles away at Puerto Caballo by seamen and marines from the ships, a detachment of the Royal Irish Regiment and 250 Baymen to make an overland attempt on Omoa.

[citation needed] The bombardment from the sea, supplemented by fire from some guns which had been landed from Pomona, continued on the night of 19 October, occupying the garrison which did not notice storming parties of seamen, marines and soldiers infiltrating the fort.

[citation needed] The fort was one of the few structures left standing after 1974's Hurricane Fifi destroyed the town and was a point of rescue operations afterward.