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Fire officials in South Carolina were digging Wednesday through scorched wreckage of a historic black church gutted overnight under unknown circumstances.

At a news conference Wednesday, investigators said they were still determining what caused the fire Tuesday night at Mount Zion African Methodist Episcopal Church, near the rural town of Greeleyville. The collapsed roof and charred brick walls immediately brought to mind a crime 20 years ago, when the Ku Klux Klan torched that very same house of worship to the ground.

Related: Spate of Fires at Black Churches Raise Concerns of Rise in Hate Crimes

South Carolina Gov. Nikki Haley told NBC News that the fire wasn't suspicious, saying the church had been struck by lightning.

But a source close to the investigation later told NBC News: "I don't know where she got that information from."

The source said it would be about a week before state crime lab tests on samples taken from the site would be available, adding: "We did have lightning in the area, but we couldn't confirm the lightning hit the church."

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Williamsburg County Chief Sheriff's Deputy Stephen Gardner said the investigation was ongoing and also wouldn't speculate about the cause, including the heavy lightning storm that passed over the area.

Greeleyville Mayor Jesse Parker said, "We were saddened by what we saw out there," adding: "To see the church in flames again, it gives you an ill feeling. We don't know what happened."

No injuries were reported, but the fire took around 2½ hours to bring under control, the Clarendon County Fire Department said about midnight ET.

Williamsburg County Fire Chief Randy Swinton told NBC News that the 8,000-square-foot church had been destroyed in the inside.

Only the brick walls of the church remained Wednesday morning. The long slender windows no longer had glass in them, and the side of the church facing the rural highway had a white cross that appeared blackened.

In Greeleyville, S.C., where Mt. Zion African Methodist Episcopal burned on Tuesday night. pic.twitter.com/O5vhKyAUtN — Alan Blinder (@alanblinder) July 1, 2015

The State Law Enforcement Division, or SLED, and investigators from the U.S. Bureau of Alcohol, Tobacco, Firearms and Explosives were on the site overnight to review the latest in a series of fires at predominantly Southern black churches since June 17. That's when a white gunman killed nine black worshipers at Emanuel AME Church in Charleston, about 50 miles south of Greeleyville.

Hours before the Greeleyville fire, the NAACP sent a series of tweets saying it was "alerting black churches to take necessary precautions" and urging the Justice Department to "investigate a series of black church fires in the Southeast."

NAACP State Conferences and units are now alerting black churches to take necessary precautions. #WhoIsBurningBlackChurches — NAACP (@NAACP) June 30, 2015

The fires have fueled concerns about the potential for a new wave of racist violence since the Charleston shooting.

Asked whether Tuesday's fire could be related to the other recent blazes, SLED Chief Mark Keel told the Post and Courier newspaper of Charleston: "Certainly, I think we all are concerned about those things."

Mount Zion, founded more than 110 years ago, was burned to the ground June 20, 1995, by two members of the Ku Klux Klan. They pleaded guilty the following year. That arson also came amid a rash of suspicious church fires.

President Bill Clinton attended the rededication of the rebuilt church a year later and said in a speech that "it was the church that saved the people until the civil rights revolution came along."

He added that it was "doubly troubling to people ... who spent their entire lives working for equal opportunity among our people...to see our native South engulfed in a rash of church burnings."