The second suspect in the Boston Marathon bombings was taken into custody in Watertown, Massachusetts, Friday night, police said at the end of a day of intense searching that shut down daily life across a large swath of greater Boston.

Meanwhile, American Muslims braced for a backlash after the alleged perpetrators of Monday’s attack on the landmark sporting event were identified as Chechens who shared their faith. According to reports, Muslims are experiencing anew harassment and anxiety which took place after 9/11 attacks.

The second suspect, Dzhokhar Tsarnaev, 19, was found hiding in a boat just outside the area where the police had been conducting door-to-door searches all day, the Boston police commissioner, Edward Davis, said at a televised news conference Friday night.

“A man had gone out of his house after being inside the house all day, abiding by our request to stay inside,” Davis said, referring to the advice officials gave to residents to remain behind locked doors. “He walked outside and saw blood on a boat in the backyard. He then opened the tarp on the top of the boat, and he looked in and saw a man covered with blood. He retreated and called us.”

“Over the course of the next hour or so we exchanged gunfire with the suspect, who was inside the boat, and ultimately the hostage rescue team of the F.B.I. made an entry into the boat and removed the suspect, who was still alive,” Mr. Davis said. The suspect, he said,  was in “serious condition” and had apparently been wounded in the gunfight that left his brother dead.

Tsarnaev’s 26-year-old brother, Tamerlan, was killed early Friday morning after a shootout with police in another section of Watertown.

Also Friday, a report from Russian television cited the men’s mother as saying her older son had previously been interviewed by the FBI because of his interest in radical Islamic teachings. The FBI confirmed that agents in Boston had interviewed the elder Tsarnaev in 2011, on behalf of an unspecified foreign government that suspected he had ties to a terrorist organization. But the FBI found nothing warranting further investigation.

The standoff with the younger Tsarnaev began just minutes after a press conference in which authorities had conceded that a daylong search for Tsarnaev had come up empty. They had said they did not know where the fugitive was, but would still lift a “shelter in place” order anyway.

“You can get back out, as long as you are vigilant,” said Massachusetts Governor Deval Patrick.

Once captured, Tsarnaev was rushed to a hospital, where he was in serious condition. “We will determine what happened. We will investigate any associations that these terrorists may have had. And we’ll continue to do whatever we have to do to keep our people safe,” President Barack Obama said after the capture.

“Obviously, there are still many unanswered questions,” Obama said. “Among them, why did young men who grew up and studied here as part of our communities and our country resort to such violence? How did they plan and carry out these attacks? And did they receive help?”

AFP adds: Russia and the United States agreed Saturday to step up cooperation in their fight against terror in the wake of news that two ethnic Chechens were suspected of organising the deadly Boston Marathon bombings. The Kremlin said Russian leader Vladimir Putin called US President Barack Obama to once again express his condolences and discuss ways the two sides can work more closely on security in the runup to the 2014 Winter Olympic Games in Sochi.