The Defence Department on Tuesday said Ali Hamza Ahmad Sulaiman al-Bahlul of Yemen and Ibrahim Ahmad Mahmud al-Qusi of Sudan were charged with a single count each of conspiracy to commit war crimes and will be brought to trial before a military tribunal.
They are described as having close ties to al-Qaida leader Usama bin Ladin.
Pentagon spokesman Major John Smith said prosecutors do not plan to seek the death penalty against either man if convicted.
Both are among the between 650-800 detainees imprisoned at the US naval base at Guantanamo Bay, Cuba.
In a statement, the Pentagon identified al-Bahlul as a "key al-Qaida propagandist who produced videos glorifying the murder of Americans to recruit, inspire and motivate other al-Qaida members" to attack Americans, the United States and other countries.
The Pentagon described al-Qusi as a key al-Qaida accountant and weapons smuggler who was "a long-time assistant and associate of bin Ladin dating back to the time when bin Ladin lived in Sudan."
The Pentagon said both men have served as personal bodyguards for bin Ladin.
Military tribunals will be held
at the base in Cuba
The military tribunals are expected to take place at Guantanamo Bay, though the brief charging documents do not indicate when.
The indictments also provide no documentation for government claims the men were "terrorist conspirators".
Military tribunals are traditionally used to try alleged war criminals, such as Nazi leaders after World War II.
They are similar to military trials known as courts-martial but share some features of ordinary civilian trials as well.
Suspects are entitled to defence lawyers and to put on a vigorous defence.
Rules of evidence are more favourable to the government, however, and the Guantanamo tribunal suspects will have only limited rights to appeal convictions.
Both are charged with conspiring with al-Qaida to commit murder and attacks on civilians and civilian targets and to commit terrorism, although that term is not further defined.
The indictments list several crimes attributed to al-Qaida, including the September 11 attacks, the 1998 bombing of US embassies in Kenya and Tanzania and the 2000 bombing of the Navy warship USS Cole.
The indictments do not allege the two men played any specific role in planning for or carrying out those attacks.