The dramatic raid came six months after Guzman fled through a tunnel from a maximum security prison in a made-for-Hollywood escape that deeply embarrassed the government and strained ties with the US.
Mexican president Enrique Pena Nieto announced the capture using his Twitter account: “Mission accomplished: we have him.”
Few had thought Guzman would be taken alive, and few now believe Mexico will want to try to hold him a third time in its prisons.
He escaped from maximum-security facilities in 2001 and on July 11 last year, the second breakout especially humiliating for the Pena Nieto administration, which held him for less than 18 months.
The capture had senior Mexican officials at a foreign ministry event gleefully embracing and breaking into a spontaneous rendition of the national anthem after interior secretary Miguel Osorio Chong delivered the news.
Guzman was held after a shoot-out between gunmen and Mexican marines at a home in an upmarket area of Los Mochis, a seaside city in his home state of Sinaloa.
The Mexican navy said that marines raided a home after receiving a tip about armed men there. They were fired on from inside the structure, it said. Five suspects were killed and six others arrested. The marine’s injuries were not life threatening.
“You could hear intense gunfire and a helicopter – it was fierce,” said a neighbour, adding that the battle raged for three hours.
Guzman may have been at the house and fled while his gunmen and bodyguards provided covering fire. The drug lord was later captured at the hotel Doux, a low-rise modern building on the outskirts of town.
Some reports said he tried to escape through storm drains. In 2014, Guzman evaded capture by fleeing through a network of interconnected tunnels in the drainage system under Culiacan, the Sinaloa state capital.
Marines seized two armoured vehicles, eight rifles, one handgun and a rocket-propelled grenade launcher at the home in Los Mochis.
