Attorney General Loretta Lynch said the "nature of the alleged crime and the resulting harm" were factors in choosing the death penalty.
Dylann Roof is charged with the murders of nine worshippers at an African-American church in South Carolina.
Police said he spent an hour sitting with parishioners before opening fire.
The 22-year-old was attending a Bible study meeting at the historic Emanuel African Methodist Episcopal Church in June when he attacked, say prosecutors.
He faces 33 federal charges, including hate crimes, obstruction of religion and firearms offences.
Police say he targeted the victims because of their race and he holds white supremacist views.
Thousands attended the funeral of one of the victims, the Reverend Clementa Pinckney.
President Barack Obama was among them, and he ended his eulogy for Mr Pinckney by singing Amazing Grace.
The tragedy reignited debate about race relations and sparked a backlash against the Confederate battle flag, after a picture emerged of the suspect carrying one.
The US justice department is seeking the death penalty in the case of the Charleston church shooting which claimed nine lives last year.