"Following the department’s rigorous review process to thoroughly consider all relevant factual and legal issues, I have determined that the Justice Department will seek the death penalty," Attorney General Loretta Lynch announced today. "The nature of the alleged crime and the resulting harm compelled this decision."
Roof is accused of killing black worshippers at the historic Emanuel African Methodist Episcopal Church in Charleston in June 2015, armed with a .45 caliber handgun and eight magazines loaded with hollow-point bullets.
He was looking to kill black worshippers, with the goal of "fanning racial flames" around the country and as retribution for perceived slights against white people, Lynch previously said.
A federal grand jury in South Carolina has indicted Roof, now 22, on 33 counts of federal hate crimes and firearm charges. He is also facing state charges.
ABC News' Pierre Thomas and Jack Cloherty contributed to this report.