Dylann Roof, 22, allegedly joined an evening Bible study class at Emanuel African Methodist Episcopal Church in Charleston, then shot participants with a .45-caliber Glock handgun. Three people survived the shooting.
He has been indicted for the killings in both state and federal court. It is not yet clear when the federal trial will begin.
"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," US Attorney General Lynch said in a statement yesterday.
In a separate filing in US District Court in Charleston, federal prosecutors listed several aggravating factors they said justified execution.
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Roof "has expressed hatred and contempt toward African Americans, as well as other groups, and his animosity towards African Americans played a role in the murders," read the seven-page filing entered by Assistant US Attorneys Julius Richardson and Nathan Williams.
The document also noted Roof "demonstrated a lack of remorse" and "targeted men and women participating in a Bible study group at the Emanuel AME Church in order to magnify the societal impact."
Roof was arrested in North Carolina a day after the shooting.
A website attributed to him was later found to contain racist views toward African Americans, as well as photographs of Roof brandishing guns and the US South's historic Confederate battle flag.
In July, Roof pleaded not guilty to a 33-count indictment returned by a federal grand jury including charges under a hate crime law that prohibits the use of force to harm an individual on the basis of race or colour.
He is also charged under a second hate crime law that bans the use of force to prohibit the free exercise of religious belief. In addition, he stands accused of using a firearm to carry out what Lynch has called "racially motivated murders and attempted murders.