CHARLESTON, S.C. — Dylann Roof, 21, has been captured in Shelby, North Carolina, after a massive manhunt in connection with the shooting deaths of nine people at a historically black church in Charleston, South Carolina.

He was apprehended during a traffic stop, after police were alerted some type of “suspicious activity,” authorities said.

Charleston Police Chief Greg Mullen said Roof “obviously committed a tragic, heinous crime last night in the city of Charleston.”

He credited “unparalleled cooperation” between law enforcement agencies for the quick arrest.

Chief Mullen said Roof was taken into custody without incident.

Earlier Thursday, police released photographs of the young, white man suspected of being the gunman who shot and killed nine people at a historic black church during a Wednesday night prayer meeting.

The FBI said it was searching for Dylann Roof, 21, Thursday morning, and noted he was 5-foot-9, and approximately 120 pounds, and that he he may be driving a black 2000 Hyundai Elantra sedan.

He was apprehended about two hours later.

Roof has been arrested twice as an adult, one a drug-related offense and the other a trespassing charge. He was out on bond at the time of the shooting rampage, court records show.

The Justice Department’s Civil Rights Division, the FBI and the U.S. Attorney’s Office for the District of South Carolina are opening a hate crime investigation into the shooting.

The suspect joined the prayer group inside the church for an hour before opening fire at about 9 p.m. Wednesday, Chief Mullen said.

The deadly attack at Emmanuel AME church, one of the oldest black church in the country, shook Charleston and sent shockwaves across the country.

Speaking on the floor of the U.S. House, Rep. Jeff Duncan, South Carolina Republican, asked lawmakers to please pray for the 180-year-old Emanuel African Methodist Episcopal Church and those impacted by the shooting.

“Tragedy shot through the heart of every family and community last night in South Carolina,” Mr. Duncan said. “It is important at times like these to remember that we are all made in the image of God. We are all brothers and sisters in Christ and are there to share the burden of tragedy and loss.

“We all need to come together with compassion and love,” he said.

Republican presidential candidate Jeb Bush canceled a campaign event Thursday morning in Charleston because of the shooting.

Sen. Lindsey Graham, another 2016 GOP presidential candidate, said he was cancelling scheduled campaign stops in Philadelphia and New Hampshire this weekend in order to return home.

Sen. Tim Scott said on Thursday that he wanted “swift justice” for those who were killed during the shooting. The South Carolina Republican made the comments after catching a flight from Washington, D.C., to his home state Thursday morning.

“The horror that occurred at Mother Emanuel last night has truly devastated our community,” Mr. Scott said in a statement. “Emanuel AME means so much to so many, and we stand by them today as they mourn the loss of their leader and brothers and sisters in Christ. Pastor Pinckney was a good man, an honest man and a wonderful representative for his congregation.”

The Rev. Al Sharpton, who has been a fixture at scenes of racial unrest, said he was likely heading to Charleston.

“I will do whatever is helpful to the families and the situation,” Mr. Sharpton told MSNBC, where he works as an on-air personality.

Chief Mullen said that investigators did not know if the suspect was still in the Charleston area. He said local, state and federal law enforcement agencies on the East Coast had been alerted to be on the lookout for the suspect.

The FBI was assisting the investigation, he said.

“We’ve got a good starting point here. We’ve got a good suspect and what we need now is to get the assistance of the community,” he said.

After the shooting, groups gathered for prayer vigils outside the church.

Community organizer Christopher Cason said he felt certain the shootings were racially motivated.

“I am very tired of people telling me that I don’t have the right to be angry,” Mr. Cason said. “I am very angry right now.”

Charleston Mayor Joseph P. Riley called the shooting “the most unspeakable and heartbreaking tragedy.”

“The only reason that someone could walk into a church and shoot people praying is out of hate,” Mr. Riley said told reporters Wednesday night. “It is the most dastardly act that one could possibly imagine, and we will bring that person to justice. … This is one hateful person.”

When police arrived on the chaotic scene Wednesday night, they found eight people shot dead inside the church. Another victim died later at a nearby hospital, police said.

State Sen. Clementa Pinckney, who served as a pastor at the church, was among those killed, The Associated Press reported.

Pinckney 41, was a married father of two who was elected to the state house at age 23, making him the youngest member of the House at the time.

The attack came two months after the fatal shooting of an unarmed black man, Walter Scott, by a white police officer in neighboring North Charleston that sparked major protests and highlighted racial tensions in the area. The officer has been charged with murder, and the shooting prompted South Carolina lawmakers to push through a bill helping all police agencies in the state get body cameras. Pinckney was a sponsor of that bill.

In a statement, Gov. Nikki Haley asked South Carolinians to pray for the victims and their families and decried violence at religious institutions.

“We’ll never understand what motivates anyone to enter one of our places of worship and take the life of another,” she said.

The police chief urged people to phone in tips to a hot line: 1-800-CALL-FBI.

“Regardless of how small people think that the information they have might be, we want them to call us,” he said. “We have investigative teams that are ready to go out and follow every lead sent in to this hotline number. And that’s what we really need at this point.”

​He said tips had already come in from across the county.​

— Staff Writers Seth McLaughlin and Maggie Ybarra contributed to this report.

• This article is based in part on wire service reports.

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