The Justice Department had previously charged al-Marri with credit card fraud, false statements and identity fraud, but the government dropped those charges before his transfer to the Navy brig.
After the Justice Department secured the February indictment against al-Marri, President Obama directed Secretary of Defense Robert Gates to transfer him to federal custody.
Al-Marri had challenged his detention without charges, and the Supreme Court agreed to hear arguments in the case this spring. But when the case moved into the criminal justice system, the Justice Department petitioned the high court to drop the case, deeming al-Marri's argument moot as he was no longer being held without charge. The Supreme Court agreed and dismissed the case in March.
Jonathan Hafetz, an attorney with the American Civil Liberties Union and attorney for al-Marri, noted in a statement that the indictment "represents an important step toward restoring the rule of law," but he opposed the Justice Department's request to drop the Supreme Court case because it would leave the issue undetermined for future cases.
"The government has still not renounced the legal authority that led to Mr. al-Marri's detention in military custody for more than six years without charge or trial," Hafetz said in the March statement. "The Court should make clear that there is no legal authority for the president to deprive individuals living in the United States of their most basic constitutional rights by declaring them 'enemy combatants.'"
The ACLU claims that while in custody at the Charleston naval brig, the U.S. government held al-Marri incommunicado for more than a year and subjected him to torture and other abuses.
Court records filed that challenged al-Marri's military custody indicate that there were videotapes of the interrogations at the brig, but the Defense Department has declined to release any tapes to al-Marri's lawyers or to the public.
The move to charge al-Marri was widely expected in the legal community, in part because of the unique and narrow aspects of his case, as he was the only legal resident alien in detention in the United States without charges against him.
In a story in The New Yorker published earlier this year, al-Marri said through his lawyers that he is "not asking to be taken at my word and to be released, although I very much want to go home to my family."
He said he wanted "to be treated like every other person in the United States who is accused of a crime, including terrorism, and to be given a fair trial in an American court."
ABC News' Jan Crawford Greenburg and Ariane de Vogue contributed to this report.