Two law-enforcement officials said the suspect, Dzhokhar A. Tsarnaev, 19, was found in a boat parked behind a house there. It was not immediately clear what condition he was in.
A police officer at the scene said the man was covered in blood when he was captured. An ambulance was there. The Boston Police Department announced on Twitter: "Suspect in custody. Officers sweeping the area." And Mayor Thomas M. Menino posted, "We got him."
As about 30 law enforcement officers - wearing helmets - walked away from the scene of what had been a tense standoff only minutes earlier, neighbors who had gathered on an adjacent street applauded and shouted, "Thank you! Thank you!"
The apparent discovery of Tsarnaev came just over 26 hours after the FBI circulated pictures of him and his brother Tamerlan and called them suspects in Monday's bombings, which killed three people and wounded more than 170. The case unfolded quickly - and lethally - after that. Law-enforcement officials said that within hours of the release of the pictures, the two men shot and killed a campus police officer at the Massachusetts Institute of Technology, carjacked a sport utility vehicle, and led police on a chase, tossing several pipe bombs from their vehicle.
Then, early Friday morning, the men got into a pitched gunbattle with the police in Watertown in which more than 200 rounds were fired, and a transit police officer was critically wounded. When the shootout ended, Tamerlan Tsarnaev, 26, a former boxer, had been shot and fatally wounded. He was wearing explosives when he was killed, several law enforcement officials said. But his younger brother, Dzhokhar, managed to escape - running over his brother as he sped away, the officials said.
The disappearance of Dzhokhar Tsarnaev, and fears that he could be armed with more explosives, set off one of the most intense manhunts in recent memory. SWAT teams and Humvees rolled through quiet residential streets. Military helicopters hovered overhead. Bomb squads were called to several locations. And Boston - New England's largest city - was essentially shut down.
Transit service was suspended all day. Classes at Harvard University, MIT, Boston University and other area colleges were canceled. Amtrak canceled service into Boston. The Red Sox game at Fenway Park was postponed, as was a concert at Symphony Hall. Gov. Deval Patrick of Massachusetts urged residents to stay behind locked doors all day - not lifting the request until shortly after 6 p.m., when transit service in the shaken, seemingly deserted region was finally restored.
As the hundreds of police officers fanned out across New England looking for Dzhokhar Tsarnaev, investigators tried to piece together a fuller picture of the two brothers, to determine more about the bombing at the Boston marathon.
The older brother, Tamerlan Tsarnaev, was interviewed by the FBI in 2011 when a foreign government asked the bureau to determine whether he had extremist ties, according to a senior law enforcement official. The government knew he was planning to travel there and was afraid he might be a risk, the official said.
The official would not say which government made the request, but his father said that he had traveled to Russia last year.
"They had something on him and were concerned about him and him traveling to their region," said the official. The FBI conducted a review, examining websites that he had visited, trying to determine whether he was spending time with extremists and ultimately interviewing him. The FBI concluded that he was not a threat. "We didn't find anything on him that was derogatory," the official said.
Now officials are scrutinizing that trip, to see if he might have met with extremists while abroad.
The rapid developments began Thursday night, when the two men are believed to have fatally shot an MIT police officer, Sean Collier, 26, in his patrol car, the Middlesex County district attorney's office said. Soon after that, a man was carjacked nearby by two armed men; when he was released he told investigators that the men who took his vehicle said they were responsible for marathon bombings, a law enforcement official said. Police went off in search of his car, and a frenzied chase began.
Police and the suspects traded gunfire and "explosive devices were reportedly thrown" from the car by the suspects, the district attorney's office said. A transit police officer, Richard H. Donohue, was shot and critically wounded.
After a pitched gunbattle with police, the older brother, Tamerlan Tsarnaev, was fatally shot; the younger brother, Dzhokhar, managed to get away.
One law enforcement official said Dzhokhar Tsarnaev was wounded, and two other officials said authorities had tracked him at some point during the manhunt by his blood trail.
An uncle of the men, Ruslan Tsarni, who lives in Montgomery Village, Md., told reporters that he was ashamed of their actions, bitterly calling them "losers" and sternly denouncing the bombings. And he urged the surviving brother to turn himself into authorities.
"I say Dzhokhar, if you're alive, turn yourself in and ask for forgiveness," said Tsarni, who said his family had been estranged from the brothers', and that the brothers' father, who recently moved back to Russia, had worked "fixing cars" in America.
For much of Friday a virtual army of heavily armed law enforcement officers went through houses in Watertown, outside Boston, one by one in a search for Dzhokhar Tsarnaev. Police had blocked off a 20-block residential area and emphatically urged people there to stay inside their homes and not answer their doors.
Boston Police Commissioner Edward Davis said: "We believe this to be a man who's come here to kill people, and we need to get him in custody."
In Washington, as well as in the Boston area, law enforcement and counterterrorism officials were struggling to determine whether the brothers had any accomplices still at large and whether they had any connections to foreign or domestic terrorist organizations.
One law enforcement official said the FBI and police were seeking "a number of people with whom we would like to speak in furtherance of the investigation."
Asked if any were suspected accomplices or co-conspirators, the official would say only that investigators were "not ready to classify anyone yet."
Several law-enforcement officials, asked about the tactics apparently employed by the brothers, said that despite the devastation they are suspected of causing at the marathon, the death of one police officer and grievous wounding of another, their planning appeared, at least at this point, to be flawed.
"They didn't practice tradecraft," said one official, a veteran counterterrorism investigator who has been briefed on the case. "Listen, I just don't understand how anybody could do something like that and basically go home and expect that they wouldn't get caught."
As the manhunt grew in intensity, law enforcement officials throughout New England tried to chase down leads.
After the authorities in Boston notified transit police officials that there was a possibility that Dzhokhar Tsarnaev had boarded the last Amtrak train from Boston bound for New York City early Friday, the train was searched between stations in Connecticut, according to an official with knowledge of the matter. Investigators reviewed video surveillance footage from the stations in Providence, R.I., and New Haven and New London, Conn., to make sure that he had not gotten off the train before it was stopped.
The last place he was seen was Watertown, where the two men got into a pitched gunbattle with the police.
A Watertown resident, Andrew Kitzenberg, 29, said he had looked out his third-floor window to see two young men of slight build in jackets engaged in "constant gunfire" with police officers. A police SUV "drove towards the shooters," he said, and was shot at until it was severely damaged. It rolled out of control, Kitzenberg said, and crashed into two cars in his driveway.
Meanwhile, Kitzenberg said, Dzhokhar Tsarnaev got back into his car, turned it toward officers and "put the pedal to the metal."
The car "went right through the cops, broke right through and continued west."
Tamerlan Tsarnaev was critically injured with multiple gunshot wounds and taken to Beth Israel Deaconess hospital in Boston, where he was pronounced dead at 1:35 a.m., officials said.