Mohammed Ahmed Haza al-Darbi could face life in prison if convicted, the U.S. Department of Defense said.
The charges, filed Wednesday, alleged that al-Darbi, 47, "aided and abetted" an attack against the ship, MV Limburg, in which a number of civilians were injured.
A Bulgarian crew member died in the attack, The Miami Herald reported.
The Defense Department statement said al-Darbi joined al-Qaida in 1997 and attended terrorist camps run by the organization in Afghanistan. He was a weapons instructor at one of the camps, officials allege.
From 2000 to 2002, the statement adds, al-Darbi supported efforts by al-Qaida groups to bomb commercial oil tankers in the Strait of Hormuz and off the coast of Yemen.
Al-Darbi was captured in Azerbaijan and brought to the U.S. base at Guantanamo Bay, Cuba, in August 2002, two months before the attack on the MV Limburg.