Police said he has been charged with nine counts of murder and one weapons possession charge.
South Carolina’s Governor, Nikki Haley, said the 21-year-old should face the death penalty if convicted.
Mr Roof was detained more than 200 miles away in North Carolina and flown back to Charleston.
Reports say the victims of the shooting included a state Senator.
America’s President, Barack Obama, while speaking on Thursday, described the event as yet another tragedy caused by guns in the society.
President Obama said Americans had to confront the fact that frequent incidents of gun violence do not occur in other advanced countries.
He also said that he and his wife, Michelle, knew Reverend Clementa Pinckney who was killed along with eight others on Wednesday night.
Meanwhile, the Police are treating the killings as a hate Crime.
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