The US Department of Justice has indicted Dylann Roof on 33 federal charges, including nine murders, three attempted murders and gun charges.
Mr Roof specifically sought out an African American church for his crimes, US Attorney General Loretta Lynch said.
The 21-year-old could face the death penalty if convicted.
"Racially-motivated violence such as this is the original domestic terrorism," Ms Lynch said.
Mr Roof is accused of killing nine black parishioners after joining their bible study at the Emanuel AME Church in Charleston on 17 June.
Pictures later emerged online of him holding the Confederate battle flag, sparking a backlash against the emblem, which to many is a symbol of slavery.
The government is charging Mr Roof under a hate crime law that bans the use of force to harm individuals based on race.
He is also charged under another hate crime law that bans use of force to prohibit religious freedom and worship.
Conferring with victims' families about possible use of the death penalty will be "an important part of the decision-making process", said Ms Lynch.
South Carolina does not have hate crime laws, but the state's murder charges against Mr Roof make the death penalty a possibility.
The man accused of killing nine black churchgoers in Charleston faces dozens of federal charges, including hate crimes.