Members at the Emanuel African Methodist Episcopal Church in downtown Charleston had gathered for a prayer meeting when gunfire erupted in the 19th century building, raising racial tensions in the country that has recently witnessed a spate of killings of unarmed black men by white police officers.
The killings had led to widespread protests and riots besides a national debate on race.
Police has released images of the suspected shooter captured from the CCTV that show him about 5 feet 9 inches tall with dark blond or brown hair in a distinctive bowl-type haircut.
The suspect was seen leaving the church in a black sedan, police said.
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"At this point, we have nine victims in this hideous crime that has been committed," Charleston Police Chief Gregory Mullen told reporters.
A woman survivor told family members that the gunman initially sat down in the church for a bit before standing up and opening fire, local media The Post and Courier reported.
The gunman reportedly told the woman he was letting her live so she could tell everyone else what happened.
The church's 41-year-old pastor, state Senator Clementa Pinckney, was among eight persons who died inside the church, while another person was declared dead at hospital.
The FBI will aid the investigation, Mullen said.
"This is an unspeakable and heartbreaking tragedy in this most historic church, an evil and hateful person took the lives of citizens who had come to worship and pray together," Charleston Mayor Joe Riley said in a statement.
"While we do not yet know all of the details, we do know that we'll never understand what motivates anyone to enter one of our places of worship and take the life of another," she said in a statement. "Please join us in lifting up the victims and their families with our love and prayers."
No information has been released yet about the victims of one of the worst mass shootouts in the history of the State.