The FBI has been working with the National Weather Service to determine whether the heavy storms in the area contributed to the fire. A forensics report of lightning strikes by CNN meteorologists shows four strikes occurred in the immediate vicinity of the church, all at 7:18 p.m. ET Tuesday.
The officials said investigators found no accelerants, an indicator of arson, at the scene.
When the current one was ready for dedication in 1996, then-President Bill Clinton visited the small town to call on the nation
to unite around race.
By early Wednesday, only the brick walls were left of that second building. The flames gutted the interior and collapsed the roof. Their remains smoldered as investigators began their work.
ATF, FBI investigate
About 50 firefighters, local police, the FBI and five agents from the Bureau of Alcohol, Tobacco, Firearms and Explosives are investigating. The Sheriff's Office and state police are also pitching in.
"Anytime there is a house of worship involved in a fire, ATF is automatically assigned to look into the cause," said agency Special Agent Tom Mangan.
Regardless of the cause of Tuesday's blaze at the church about 65 miles north of Charleston, "it was another punch to the gut" to the community, said former state Rep. Bakari Sellers on CNN Wednesday.
"This community has been through so much," he said, alluding to April 4 shooting death of Walter Scott by a white police officer, who has been charged with murder, and the Charleston church massacre in June.
"We are weary," he said. "We are tired."
"It's devastating to put the church and the community through the same thing," Greeleyville Mayor Jesse Parker told CNN. "To see it back in flames in such a short span of time is hurtful to the entire community."
The blazes were part of a spate of about 30 fires that swept black churches in Southern states at the time.
Senior Bishop John Bryant of AME's national headquarters said Tuesday night's fire "will not send us into despair or depression. As Christians, we are a people of resurrection and even from the ashes we will rise."
Rush to judgment
The hate crimes of the past have fueled suspicion among many that the recent spate of church fires must be the result of hate crimes, despite early indications that most of them might not even be arson, let alone steeped in racial animosity.
It's a natural reaction "because of the potent political message it sends when groups such as the Klan commit these acts. That explains the visceral reaction," Philadelphia-based writer and activist David Love told CNN.
Writing for the historically black newspaper, Atlanta Blackstar
, last week, Love noted that since the days of slavery and through the civil rights movement, white supremacists have targeted black churches because of what they stand for -- "a pillar of the Black community, the center for leadership and institution building, education, social and political development and organizing to fight oppression. Strike at the Black church, and you strike at the heart of Black American life."
So, it makes sense that even though only one in about six church fires is ruled intentional, according to National Fire Protection Agency figures, suspicions would spike each time an African-American church is reduced to cinders. In that way, he told CNN during a phone interview, white supremacists have succeeded.
"That's the goal, is to instill fear and to draw attention so that people don't forget," he said. "It may not be arson now, but people look at the cases where it actually did happen and feel, 'It could happen again.' "
It doesn't help that the authorities investigating the church fires belong to some of the same governments that have historically oppressed black people -- whether it was failing to protect rights, turning a blind eye to Klan violence or actively spying on and infiltrating groups fighting for equality during the civil rights movement, he said. More recently, a rash of police killing black men has served only to bolster distrust.
"All of it is connected, and it speaks to a lack of trust between police and the community," he said.
Asked whether he was skeptical of the early police findings that most of the fires might not be criminal acts, Love responded that "a healthy dose of skepticism" is a good thing, but he advised analyzing each case on its own merits.
"It's always important to keep one's eyes open. If (authorities) have the information, and we don't have any reason to believe they're hiding something, I'm inclined to give them the benefit of the doubt, if there's no evidence of a coverup," he said.
-- June 26: Greater Miracle Apostolic in Tallahassee, Florida. The fire was likely caused by a tree limb falling on power lines.
-- June 26: Glover Grovery Baptist in Warrenville, South Carolina. The cause has not been determined, but investigators observed no element of criminal intent.
-- June 24: Briar Creek Road Church in Charlotte, North Carolina, which houses both black and Nepalese congregations. Fire investigators ruled that fire an arson, and though they have not seen evidence that hate was a motivation for the crime, they are not ruling it out.
-- June 21: College Hill Seventh-day Adventist in Knoxville, Tennessee. Investigators ruled it an arson but they say nothing so far has indicated a hate crime. ATF and other agencies said that it looked like vandalism.
-- June 21: God's Power Church of Christ in Macon, Georgia. Investigators believe the blaze might be arson. ATF is investigating but no ruling has been made. The church had recently been broken into and air conditioners and sound systems stolen.
Most recent religious targets of hate crimes have been synagogues and mosques, the Southern Poverty Law Center said.
Firefighters battled blazes at more than 1,700 religious structures per year between 2007 and 2011, according to a 2013 report from the National Fire Protection Association
. These included houses of worship of all religions as well as funeral parlors and religious schools.
Nearly a third of the fires were caused by cooking devices. Almost a quarter started in kitchens or cooking areas. Electrical lines or lighting cause 10% of the fires.
About 16% were intentionally set, and these caused about 25% of the reported property damage, the report said.
The number of fires at religious institutions has dropped dramatically since 1980. Before then, twice as many structures burned each year, on average.