The suspect, who police described as a 21-year-old white man wearing a sweatshirt, jeans and boots, was still at large hours after the shooting on Wednesday evening.
Eight victims were found dead in the church, Chief Gregory Mullen told reporters at a media conference, and a ninth person died after being taken to a hospital. One other person was wounded and receiving treatment.
Mullen said, "It is unfathomable that somebody in today's society would walk into a church when people are having a prayer meeting and take their lives."
None of the victims were immediately identified. But the Reverend Al Sharpton, the New York-based civil rights leader, said in a Tweet that the Reverend Clementa Pinckney, the church's pastor and a member of the state Senate, was among the fatalities.
The shooting occurred at the Emanuel AME Church in the historic centre of downtown Charleston around 9 pm (0100 GMT), according to Charleston Police Department spokesman Charles Francis.

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