A grand jury returned a 33-count indictment against Roof, Lynch said at a news conference. He was indicted for federal hate crimes and firearms charges for killing and attempting to kill African-American parishioners at the Emanuel African Methodist Episcopal Church "because of their race and in order to interfere with their exercise of their religion," Lynch said.
"As set forth in the indictment, several months prior to the tragic events of June 17, Roof conceived of his goal of increasing racial tensions throughout the nation and seeking retribution for perceived wrongs he believed African-Americans had committed against white people," Lynch said.
"To carry out these twin goals of fanning racial flames and exacting revenge, Roof further decided to seek out and murder African-Americans because of their race. An essential element of his plan, however, was to find his victims inside of a church, specifically an African-American church, to ensure the greatest notoriety and attention to his actions."
The move has been expected since the 21-year-old's arrest after the June 17 shootings at the downtown Charleston church.
Federal officials have previously said that the shootings generally meet the legal requirements for a hate crime and that federal charges were likely. Roof, who is white, appeared in photos waving Confederate flags, and survivors told police that he hurled racial insults during the attack.
Roof already faces state charges including nine counts of murder. State prosecutors have not said whether they'll seek the death penalty.
Lynch also said no decision has been made on whether to seek the death penalty in this case in connection with the federal charges.