Churchgoers held hands, prayed, and hugged at the Twelfth Baptist Church in Roxbury on Thursday. When the Rev. Jeffrey L. Brown, the associate pastor, called for peace, the congregation responded with cries of “yes!”
“If we don’t begin to address the problems of racial intolerance and racial insensitivity, if we don’t begin to do that together, we will suffer at our own peril,” Brown said. “The greatest enemy that stops us from coming together is our inaction and our desire to cling on to business as usual.”
After a white gunman shot and killed nine black worshippers at the Emanuel African Methodist Episcopal Church in Charleston, S.C., on Wednesday, anguish and outrage swept across Boston. But the city’s black churches felt the sharpest blow.
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Stunned parishioners and pastors gathered to mourn that a sanctuary like theirs had become a scene of bloodshed and to decry the racism that appeared to have fueled the attack.
Rev. Mark V. Scott, the associate pastor at Azusa Christian Community in Dorchester, called the shooting “an act of terror” and described those who lost their lives in South Carolina as “martyrs.”
Time and again over the past year, as protesters have marched in Ferguson, Mo., Baltimore, and New York, Boston’s pastors have sought to help their parishioners make sense of anger and grief.
Now, after a massacre that targeted African-Americans at a prayer meeting in a church with ties to the early abolitionist movement, many said they were struggling to comprehend violence in a sacred space regarded as a monument to the resilience of the black community.
“It’s been mother of all the AME churches in the South,” said James Arthur Holmes, a professor of church history at Shaw University in Raleigh, N.C.
The church, Holmes said, was founded by black worshippers who had been turned away from a white church and was set on fire after Denmark Vesey, one of its founders, organized a slave rebellion in 1821. “That church knows adversity,” he said.
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The Rev. Gregory G. Groover Sr., pastor of the Historic Charles Street AME Church in Roxbury, said he had worshipped at the Charleston church and knew its pastor, the Rev. Clementa C. Pinckney, who was killed in the attack.
“I can’t even find the words. I’m still stunned,” he said.
Groover said his church would host a prayer service for the victims on Sunday.
“We have to get together and see each other and pray as one community for the healing and for the families of victims,” he said. “And also pray for the sickness in society, the hatred, and the racism, that someone would have it in his mind to walk into a church, of all places, and have charted in his mind to kill anyone who attends.”
Rev. Ellis I. Washington, pastor of St. Paul AME Church in Cambridge, said he’d spent the day fielding phone calls from parishioners asking, “What are we going to do?” and from people from the religious community expressing support and love.
“That church is going to be torn apart for quite some time,” he said, as a newscast about the shooting played on the TV in his office. He said he’d tried to avoid watching the news all day. “I just wasn’t ready,” he said.
St. Paul had a 7 p.m. service scheduled and was planning to open its doors an hour before. The church was to be guarded by Cambridge police, Washington said. He said he hopes church members feel safe.
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“These things are hard to deal with,” Washington said. “When you go to a church, a school, a movie theater, you have no thought of facing danger.”
Mayor Martin J. Walsh and police Commissioner William B. Evans said they had contacted clergy in Roxbury and Dorchester Thursday to express their condolences and assure them of an increased police presence.
“They’re working together to make sure everything is secure in light of South Carolina,” said Officer Rachel McGuire, a police spokeswoman. But many were still worried. “My fear and my concern is that people will not feel safe in this sanctuary, and that’s not right,” Brown said.
Groover said he, too, was concerned but determined to keep his church open and accessible. “We are a household of God, and a place of worship, and we must be that place where people can come and find refuge,” he said.
One of Groover’s parishioners, Annie Ravenell, 67, was anxiously watching the news to see if she recognized any of the names of the dead. She said she has family members who attended the Charleston church and had met pastor Pinckney at family reunions.
“I’m real worried, real worried,” she said. “It’s like my whole family is calling and everybody knows everybody in a coastal town like that.”
On Thursday night, people of all races, religions, and ages packed Bethel AME Church in Jamaica Plain for a vigil and service to remember the South Carolina victims.
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“We’re shocked but not shattered,” the Rev. Ray Hammond, the church’s senior pastor, told those in attendance.

The congregation managed to find some joy, singing loudly to hymns and swaying to music. But Wednesday’s massacre hit home for many.
“I felt like I was being attacked because I’m a black Christian,” said Movelle Lamming, who attended the service.
A message of perseverance also permeated the church.

“We’re here to affirm that we’re not backing down,” said co-pastor the Rev. Gloria White-Hammond. “We’re not shrinking back.”
In the basement of the Charles Street church, where parishioners were working at a food pantry Thursday, Thomas Lindsay, 87, said the attack recalled the violence he had witnessed growing up in Birmingham, Ala. The massacre, he said, ranks among the worst tragedies in his lifetime.
“It was tough, but nothing like this ever happened,” Lindsay said. “Black people seem to have a hard time in this country.”
The Rev. Alvan N. Johnson Jr., pastor at Grant AME Church in Boston, said the Charleston attack should not be viewed an isolated incident, but as part of a larger history of “all the violence in this country.”
“This alleged perpetrator does not represent all of white America,” Johnson said. “There are as many white people who are agonizing over this tragedy as there are black. We all must come together now and absolve the problem of violence in our society. We need to work together.”
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Steve Annear of the Globe staff contributed to this report. Monica Disare can be reached at monica.disare@globe.com; Sara DiNatale can be reached at sara.dinatale@globe.com.