Republicans today welcomed the news but were quick to pounce on the Obama administration's decision that they say is long overdue.
"It's unfortunate that it took the Obama administration more than two years to figure out what the majority of Americans already know: that 9-11 conspirator Khalid Sheikh Mohammed is not a common criminal, he's a war criminal," House Judiciary Committee Chairman Lamar Smith, R-Texas, said in a statement. "I hope the Obama administration will stop playing politics with our national security and start treating foreign terrorists like enemy combatants."
While Congress and the administration have worked to reform how military commissions proceed, there are a lot of questions about how they will work, especially whether the conspirators can be executed if they plead guilty.
"I think the death penalty can certainly be sought," Holder said today. "It's an open question about whether or not somebody can plead guilty in a military commission and still receive the death penalty. That, I think, is still an open question."
Mohammed said in December 2008 that he wanted all of the conspirators to plead guilty but it is unclear how things will proceed.
"We'll have to see how it plays out," Holder said.
Obama first announced his decision to resume military tribunals at Guantanamo Bay in March, after fierce, bipartisan resistance over trying suspects in U.S. courts.
The $725 billion National Defense Authorization Act that Obama signed Jan. 7 explicitly prohibits the use of Defense Department funds to transfer detainees from Guantanamo Bay in Cuba to the United States or other countries. It also bars Pentagon funds from being used to build facilities in the United States to house detainees, as the president originally suggested.
The move essentially barred the administration from trying detainees in civilian courts. The president objected to the provision in the bill before signing it, calling it "a dangerous and unprecedented challenge to critical executive branch authority" but also said his team would work with Congress to "seek repeal of these restrictions."
There are about 170 prisoners remaining at the detainee center in Guantanamo Bay, 30 of whom were due to face trial in criminal courts or before military commissions. Since 2002, 598 prisoners have been transferred to other countries.
Critics of military commissions say the Justice Department's decision sends the wrong signals.
"It's alarmingly premature for the government to decide on military commission trials for these defendants when substantial questions remain as to the legality and legitimacy of these tribunals," said Stephen I. Vladeck, a constitutional law expert and law professor at American University Washington College of Law.
"Sending these high-profile and critically important cases to such a thoroughly untested system, as opposed to the well-established civilian courts which have time and again proved their ability to handle terrorism prosecutions, sends exactly the wrong message about the rule of law in the United States," he said.
Today's decision by the Obama administration comes on the same day the Supreme Court refused to step in and hear appeals from Guantanamo detainees challenging their detention, signaling that the nation's highest court does not want to get involved with how the lower court is dealing with legal issues involving detainees.
ABC News' Ariane de Vogue, Luis Martinez, Pierre Thomas and Richard Esposito contributed to this report.