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Mourners arrive for the funeral of Myra Thompson, one of the nine people killed in a mass shooting in Charleston, S.C., on June 17.

TRAVIS DOVE/NYT

Martin Luther King, Jr. once said that the most segregated hour in the United States was 11:00 on Sunday morning.

That remains just as true a half century later. Though some integration has come to the schools, the military and the workplace, white and black Americans still mostly worship apart.

The "Holy City" of Charleston, so named for its scores of churches, tells the story. When a white gunman shot dead nine black parishioners at a historic black church on June 17, blacks and whites came together in mourning, embracing in front of the church and linking hands across a local bridge. Yet inside their respective churches, there is still only limited mixing of the races.

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On any given Sunday, the city's grand old churches fill with song and prayer. When the congregation spills out onto the street afterward, the crowd is usually either overwhelmingly black or overwhelmingly white, with at best only a smattering of the other race.

The congregation at the Emanuel African Methodist Episcopal Church, where the killer struck during an evening Bible study meeting, is overwhelming black. Just around the corner at the 200-year-old Second Presbyterian Church, the congregation of about 300 is overwhelmingly white.

Asked what proportion of his flock is black, Pastor Cress Darwin says, "I don't even think you could say a proportion. It's a small number."

Standing outside the tall wooden church doors in a white dress shirt and jeans, he said that the segregation of American churchgoing is not peculiar to Charleston. "There is not that much crossover anywhere in the country. It's not just here. Because why would people go someplace else when they've grown up in a place and it's dear and familiar?"

Perhaps for that reason, there has never been a push to integrate churches like the one to integrate schools.

For generations, churches like Mother Emanuel, as it is called here, have been places of refuge from hardship and prejudice.

Carly Adams, 47, of Columbia, S.C., says that she has been attending her Baptist church for as long as she can remember. She says she goes for the sense of community and the joyous atmosphere. "You're free to sing, to get the Holy Ghost. If you feel the spirit you can get up and shout and get your groove on."

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Each major denomination has its divisions of black and white. Downtown Charleston has a mainly white Catholic church, the Cathedral of St. John the Baptist, and a mainly black Catholic church, St. Patrick. It has a mainly white Presbyterian church, James Island, and, a few blocks away, a black Presbyterian, St. James.

Charleston is far from an exception. The Washington-based Pew Research Center estimates that about 80 per cent of U.S. churchgoers go to churches where one ethnic or racial group accounts for 80 per cent of the congregation.

Valerie Cooper, an associate professor at Duke University's Divinity School who is writing a book about church segregation, argues that it says troubling things about the United States that so many black and white Americans worship apart.

Prof. Cooper, who is black, says church segregation "is so commonplace that we are not even embarrassed by it any more." She says that whenever she goes to a new town and looks for a church, people will automatically steer her to the black church.

Christianity preaches brotherhood and reconciliation, so if churches remain separate and apart, "as Christians we must not believe what we say."

It isn't just Christian Americans that should worry about segregated churches, she argues. Much of the estrangement between blacks and whites comes not from active hatred, but from people "never coming into meaningful contact with each other." Things might change if they mixed at church. But they aren't and that, she says, is a bad sign for race relations.

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"If you really want to know how we are doing on race," says Prof. Cooper, "don't look at the election of a black American president – go to a church on Sunday."

The racial divide in churchgoing has deep roots in the American past. In the days of slavery, black slaves and freed blacks often worshipped under the same roof as whites, but they were commonly segregated in a separate part of the church known as a "slave gallery."

The African Methodist Episcopal Church grew out of that kind of division. Black parishioners at the St. George's Methodist Episcopal Church in Philadelphia broke away in 1787 when the church confined them to a separate section.

After the triumph of the Union in the Civil War brought an end to slavery, blacks left white-led churches en masse. They flooded out of Protestant denominations such as the Baptist, Southern Methodist and Episcopal churches and into black churches such as the African Methodist Episcopal (or AME) and the AME Zion.

"Freedmen had had enough of the white church experience," writes Charleston author Paul Porwoll in his book on a historic local church, Saint Andrew's Parish.

"They had been given little or no say in church affairs, sat in segregated seating, and endured bland sermons, an uninspiring worship experience, and a Christian doctrine manipulated to justify slavery."

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At the time, he writes, they "embraced segregation in their worship experience; it meant freedom from white interference. Black churches would fill their praise with emotion, dancing and mysticism."

That tradition continues. It has been on view over the past few days in Charleston as the city mourned the victims of the Mother Emanuel attacks in funerals filled with song, pulsing organ music and passionate sermons.

Martin Luther King was part of that tradition. Yet when asked about the segregation of churchgoing in 1963, he said it was "tragic" and called on the church to "remove the yoke of segregation from its own body."

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