Hidden ports are concealed on the player's map until discovered. Small in size, they trade in the same commodities as other ports but are not affiliated with any government. Hidden ports are indifferent to the player's reputation and may not be attacked.

A hidden port must first be found in "Open World" sailing before appearing on the player's map. The player is rewarded with 3,000 gold upon reaching a hidden port initially, and discovered ports become valid fast travel destinations.

Alcena is located along the northern coast of South America, between Cartagena and Barranquilla.

Cortina is located just off the northern South American coast, between Coro, Fort Oranje and Fort Zoutman.

El Diablo Bay is located at the intersection of Central America and South America, near Playon and Cordobas.

Gong Town is located in the Winward Islands between Fort de France and Kingstown.

Jontly is located off the west coast of Hispaniola.

Los Bontas is located along the northeast coast of South America, between Georgetown and Paramaribo.

Los Diablos is located inland from the northeast coast of South America. It may be reached by entering the river delta near Belem.

Los Guerillas is located along the northeast coast of South America near Sao Luis.

Los Pueblos is slightly inland from the northeast coast of South America near Macapa.

Los Quatros is located inland from the northeast South American coast. It may be reached from the river delta situated between Naparima and Georgetown.

Los Smuglos is located on the north coast of Cuba.

Lost Reef is located in the Bahamas near West End and Gregory Town.

Marimba is located on an isle northwest of Cuba and southwest of Lorimers.

Matagana is located along Florida's west coast, near Tampa.

Monique Island is inland from South America's east coast and may be reached from Recife.

Motir is inland from Macapa, off the northeast coast of South America. It is recommended to reach Motir using the northern most river, as the southern passage is blocked by an isthmus.

New Loyd is located along the southern coast of North America, near New Orleans.

Olina is located along the east coast of the Yucatán Peninsula, between Cancun and Chetumal.

Ondico is located along Mexico's east coast, between Brownsville and Tampico.

Santo Bello is located along the northeast coast of South America between Paramaribo and Macapa.