Mexico recaptured the world's top drug lord Joaquin "El Chapo" Guzman in a pre-dawn shootout and chase through drains on Friday, returning him to the same prison he escaped from six months ago, in a boost for the beleaguered government.

The head of the powerful Sinaloa Cartel was captured in a car wearing a filthy vest after fleeing through tunnels and drains from a raid on a safe house in the city of Los Mochis, in his native northwestern state of Sinaloa.

"Mission accomplished: We have him," President Enrique Pena Nieto said on his Twitter account. "I want to inform all Mexicans that Joaquin Guzman Loera has been arrested."

For Pena Nieto, the capture of a trafficker who twice slipped out of Mexican prisons is a sorely-needed victory after his presidency was tarnished by graft and human rights scandals and the shame of the kingpin's flight from the maximum security Altiplano prison in July.

It also provides relief to U.S.-Mexico relations, strained by suspicion of high-level collusion given the apparent ease with which Guzman gave Mexican authorities the slip after the United States requested his extradition.

Guzman now faces possible extradition to face trial in the United States. That process could take months, although U.S. Republican party presidential hopeful Marco Rubio was among those calling for Washington to immediately pursue extradition.

Once featured in the Forbes list of billionaires, Guzman led a cartel that has smuggled billions of dollars worth of cocaine, heroin, marijuana and methamphetamines into the United States and fought vicious turf wars with other Mexican gangs.

He was caught early on Friday after Mexican marines raided his safe house, killing five and capturing six of Guzman's henchman. They pursued the drug lord through the northern city's drains and caught him after a car chase through the outskirts, Attorney General Arely Gomez said.

He was flown to Mexico City and later transferred in a naval helicopter back to the Altiplano.

Guzman, whose nickname means "Shorty", first escaped prison in 2001 by bribing prison officials, and went on to dominate the world of Mexican drug trafficking.

He was recaptured by Pena Nieto's government in 2014 but escaped in July by capitalizing on the drug-tunneling skills his cartel honed on the U.S. border. A mile-long tunnel equipped with electric lights, rails and a motorbike came out directly into the shower of his prison cell and he simply slipped away.

The escape heaped embarrassment on Pena Nieto, who had resisted a U.S. request to extradite Guzman and had said previously that an escape would be "unforgivable."

Dozens of people were arrested over the jailbreak, though details of who Guzman bribed and how his accomplices knew exactly where to dig into the prison remain scarce.

His recapture on Friday involved Mexican marines, the U.S. Drug Enforcement Administration (DEA) and U.S. Marshals, a senior Mexican police source and a U.S. source said.

After stopping his getaway car, the Marines took Guzman and waited for reinforcements at Hotel Doux, a love motel on the outskirts of town that rents out rooms by the hour.

Los Mochis residents described gunfire and explosions from about 3:30 a.m. (0930 GMT).

Schools were closed as helicopters clattered overhead.

"The teachers were coming out terrified because they had heard the rumors that he was fleeing in the city's drains," said Ana Bertotti, 30, a housewife who crossed town to find her child's kindergarten closed.

One photograph widely circulated on social media, but that could not be independently verified by Reuters, appeared to show Guzman sitting handcuffed on a hotel bed, in a room that resembled those shown on the Hotel Doux website.

He was wearing a filthy vest and a poster of a scantily clad woman was pinned on the wall behind him.

Another photo appeared to show Guzman without handcuffs and wearing the same vest in the back of a vehicle next to one of his top assassins.

U.S. officials and the DEA, which has had a bumpy relationship with its Mexican counterparts since traffickers tortured a U.S. agent to death in 1985, took no credit and congratulated Mexico on the capture.

"This notorious criminal is – and will remain – behind bars, until he faces justice in a court of law," said DEA Acting Administrator Chuck Rosenberg.

After coming under fire for failing to send Guzman to the United States before he escaped the last time, Mexico said in July it had approved an order to extradite him north of the border.

On Friday, the U.S. Justice department said its previous request to extradite Guzman to the United States still stands.

A senior Mexican official said the attorney general's office would quickly move to determine how Guzman could be extradited, but that it could be months before he was sent out of the country.

Guzman's lawyer in October appealed against possible extradition in case his client was captured.

Guzman is wanted by U.S. authorities for various criminal charges including cocaine smuggling and money laundering

In 2013, Chicago dubbed him its first Public Enemy No.1 since Al Capone, the gangster who won notoriety in the 1920s.

Believed to be 58 years old, Guzman was born in La Tuna, a village in the Sierra Madre mountains in Sinaloa state where smugglers have been growing opium and marijuana since the early 20th century.

After Guzman's first prison break, violence began to creep up in Mexico. The situation deteriorated during the 2006-2012 presidency of Pena Nieto's conservative predecessor Felipe Calderon, when nearly 70,000 people lost their lives in gang-related mayhem.

After he managed to outmaneuver, outfight or out-bribe his rivals to stay at the top of the business for over a decade, some security experts see in Guzman's capture new hope for Mexico.

"This gives important credibility to the Mexican government. And the fact is, they're starting to move forward in implementing the rule of law," said Mike Vigil, former head of global operations for the DEA.