Police have confirmed that the second Boston bombing suspect Dzhokhar Tsarnaev, is alive and in custody after a standoff in Watertown district.

A local CBS TV station cited Boston's Mayor Thomas Menino on Friday as saying a man believed to be the suspect was surrounded in Watertown.

The Reuters news agency reported that according to state police, Tsarnaev was bleeding, in serious condition and was being taken to Massachusetts General Hospital.

President Barack Obama said Tsarnaev's capture closes what he called "an important chapter in this tragedy".

Bombing suspect Dzhokhar Tsarnaev, 19, was taken to hospital in serious condition after being captured [AFP]

Obama spoke from the White House shortly after law enforcement took 19-year-old Dzhokhar into custody in a boat that was parked in a Massachusetts neighbourhood backyard. His older brother was killed earlier on Friday in an attempt to escape police.

Al Jazeera's correspondent, Alan Fisher, reporting from Boston, said that news of Dzhokhar's apprehension was met with cheers throughout Boston.

"This is a city that said 'We will not be broken, we will not be beaten by what happened'," Fisher said.

Our correspondent said that the suspect was found when the FBI had been alerted to a "trail of blood", with conflicting reports that a suspect had been pinned down.

A local man contacted the authorities, said Fisher, having noted that his shed door, where he stores the boat, was open, and saw what he thought were pools of blood.

Our correspondent said that shots were heard being fired in Watertown and that police had been telling people "stay down and stay away from windows".

Watertown resident Joseph Gerson said he had seen armed police running down his street.

Just hours earlier, Massachusetts Governor Deval Patrick lifted a stay-in-place order for Boston and mass transit reopened while police pressed ahead with a manhunt for the second suspect in the Boston Marathon bombing.

Three people died and more than 170 were hurt when two bombs exploded near the finish line of Monday's marathon in an attack seen as the worst since the events of September 11, 2001.

Watertown 'a warzone'

"It is like living in a warzone. You have to be concerned for your family," Gerson said.

Earlier, investigators were searching "door-to-door, street-to-street" in Watertown, and had searched about 60 per cent of the homes so far.

Police said they would conduct a "controlled explosion" in Cambridge, Massachusetts, later on Friday as part of their investigation into the Boston Marathon bombings.



The move was being taken "out of an abundance of caution" to protect officers conducting a search of a building, Massachusetts state police spokesman Timothy Alben said.

A national security official identified the hunted man as Dzhokhar Tsarnaev and said the dead suspect was his brother, Tamerlan Tsarneav, 26.

An uncle, Ruslan Tsarni, who lives in a Washington suburb, told The Associated Press that the men lived together and had been in the United States for about a decade.

They came from a region near Chechnya that has been plagued by an insurgency related to a separatist war.



The suspects' father told the AP his younger son was a second-year medical student and described him as "a true angel".



On Thursday night, a university police officer was killed, a transit police officer was wounded, and the suspects carjacked a vehicle before leading police on a chase that resulted in the first suspect being shot dead.

Following the developments in the night, police cordoned off the suburb of Watertown and told residents not to leave their homes or answer the door as officers in combat uniforms carrying rifles scoured a 20-block area.



Public transportation throughout the metropolitan area was suspended, and air space was restricted. Universities including Harvard, MIT and public schools were closed.

'A terrorist'



Police were searching for the younger Tsarnaev, previously known only as Suspect 2, who was shown wearing a white cap in surveillance pictures taken shortly before Monday's explosions and released by the FBI on Thursday.



"We believe this to be a terrorist," Boston Police Commissioner Ed Davis said. "We believe this to be a man who has come here to kill people. We need to get him in custody."



The older brother, previously known as Suspect 1, who was seen wearing a dark cap and sunglasses in the FBI images, was pronounced dead.



The FBI on Thursday identified the men as suspects in the twin blasts believed caused by bombs in pressure cookers placed inside backpacks left near the finish line of Monday's Boston Marathon.