Dylann Roof is charged with murdering the nine parishioners in June during their Bible study class.
Prosecutor Scarlett Wilson said the killings were "the ultimate crime" and deserved "the ultimate punishment".
The 21-year-old also faces separate federal charges of hate crimes.
The church where the killings took place is a nationally known historic black church, and federal prosecutors claim the killings were racially motivated.
After the shootings, photos emerged online of Dylann Roof holding the Confederate battle flag, sparking a backlash against the emblem, which to many is a symbol of slavery.
Ms Wilson said family members of the victims respected her decision to seek the death penalty, despite differing views on the punishment:
"Some family members of victims, because of their faith, do not believe in the death penalty under any circumstances. Some believe the death penalty is just too easy.
"Still others believe that the death penalty for the murders at Mother Emanuel Church is entirely appropriate.
"We all agree that forgiveness is an important part of the healing process but know that forgiveness doesn't necessarily mean foregoing consequences, even severe consequences," she said.
Prosecutors in the US state of South Carolina say they will seek the death penalty for a white man accused of shooting dead nine black people at a church in Charleston.