The fire left the church roofless and given lightning and storms were reported overnight in the region, authorities said it was still too early to determine the cause of the fire.
Tuesday night`s fire came as authorities in Georgia, North Carolina, South Carolina and Tennessee were investigating a string of fires at other predominantly black churches.
Though the authorities said three of the five fires were arson, investigators did not describe any of the incidents as hate crimes.
Just hours before the fire at the Mount Zion Church, some 100 km north of the Charleston church, where a white gunman shot down nine African-American churchgoers on June 17, civil rights group National Association for the Advance of Colored People (NAACP) had warned black churches around the country to beef up security.
All the six fires happened after Dylann Roof, 21, started a shooting spree on June 17 night at the Emanuel African Methodist Episcopal Church in Charleston, South Carolina. After his arrest, Roof reportedly told police that he wanted to start a "race war".
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