“Mother Emanuel,” as the church is called, has a long past in the black community of Charleston, rooted in the African Methodist Episcopal church movement of the early 1800s and spurred by attempts to segregate the Methodist Episcopal Church.

Charleston, once the slave capital of the United States, accounted for as many as 60 percent of all African-American’s family ancestors coming through the port, Johnson said. Many of the city’s black communities have direct ties to Emanuel, he added.

“In the Jim Crow era, the churches might be the only piece of architecture that the black community owned,” said Valerie Cooper, a professor of black church studies at Duke Divinity School in Durham, N.C. Segregation that insured blacks were barred from civic spaces meant churches became the hub of labor and political organization.

“It is possible that American churches were most integrated during slavery because, of course, owners could require their slaves to go to church with them where they could keep an eye on them,” Cooper said.

Churches in the south are far from integrated today, she said.

“It’s sad. It’s a testimony to racism in America that there are large numbers of essentially theologically identical denominations that are only divided by race,” Cooper said. In many southern cities, for example, there are two First Baptist churches – a black one and a white one, she said. “This history of division has to do with blacks seeking a place where they would not be treated as second class citizens,” Cooper said.

“On the one hand, black churches are used to dealing with terrorism,” she said. “This is a horrible event but there is a history of attacks on black churches and black congregants, particularly during the Civil Rights movement.”

The setting of Wednesday night’s mass shooting is layered with symbolism from generations of fighting racism.

“An AME church is a very important symbol of resistance and liberation and spirituality for black folks, especially in the South,” said Lecia Brooks, outreach director for the Southern Poverty Law Center, which tracks hate groups.

It’s that symbolism of Mother Emanuel’s legacy fighting racism, Brooks says, that proves the setting for the mass shooting was not accidental.

“This was not a random act. He was and is a white supremacist that carried out a horrible act,” Brooks said. “It was an act of domestic terrorism. If he could strike fear in the congregants of this very important and powerful symbol in the black community in the south, then it would be amplified across the south and across the country.”

While there has been a reduction of hate groups in the U.S. in recent years, there has been an increase in rhetoric of this sentiment spreading across social media. The impact, Brooks said, is that “people like this young man can be deeply influenced and moved into action in the same way, in probably more horrific ways than hate groups.”

That impact has also propagated fear throughout the city’s churches, according to Patricia Williams Lessane, an anthropologist and the director of the College of Charleston’s Avery Institute of Afro-American History and Culture. “The black church has been the one place where we felt like we have sanctuary.”

“We haven’t seen anything like this since the 16th Street bombings,” she said, referring to a turning point in the Civil Rights era when four African-American girls were killed by white supremacist in September 1963. “Folks are just reeling. There’s a deep sense of sadness, but also fear.”

In Charleston, a city that long ago earned the nickname “The Holy City” because of its historical religious tolerance, people of all faiths have been impacted by this tragedy, Lessane said.

For all its religious tolerance, however, the city remains glaringly segregated outside of houses of worship, especially in largely white, affluent tourist areas in the heart of the city, she added. Consequently, the city’s African-American community has largely been squeezed out by expanding high-rent districts and high taxes, Lessane added.

It’s a social problem that will take more than prayer vigils to solve, she said. “Don’t get me wrong, I’m not poo-pooing prayer vigils,” she said. “We have to come away with a systemic, long-term plan with some short term benchmarks that are tangible.”

“Charleston is based upon all these cultural sensibilities,” Lessane said. “People want to be nice. They want to talk about nice things. They don’t want to talk about hard topics,” like race, she said. “But we have to talk about hard topics and we can’t just talk about them, we’ve got to do something about them.”