"Mission Accomplished," President Enrique Peña Nieto announced via Twitter. "We have him."
Mi reconocimiento al Gabinete de Seguridad del Gobierno de la República por este importante logro en favor del Estado de Derecho en México.
— Enrique Peña Nieto (@EPN) January 8, 2016
Members of Mexico's navy caught Guzman in an operation at about 4:30 a.m. (6:30 a.m. ET) in the coastal city of Los Mochis in Sinaloa state, a senior law enforcement official in Mexico told CNN.
Several people aligned with Guzman died in the raid, the official said. The Mexican navy put the number of dead at five, with six others arrested. No navy personnel were killed, and only one was injured.
Peña Nieto said the recapture of Guzman culminates "days and nights" of collaborative work among Mexican intelligence and police agencies.
"They are a pride to our nation," he said, referring to the multi-agency operation in an address at the National Palace in Mexico City.
Without specifically mentioning how Guzman had already twice escaped from Mexican prisons, the Mexican President said the recapture of Guzman ought to restore Mexicans' faith in their government and justice system.
Friday's announcement marked the third time that Guzman was captured by Mexican authorities.
"The arrest today is extremely important for the security institutions of the government," the President said. "Today our institutions have demonstrated one more time that our citizens can trust them, and our institutions are at the level that has the strength and determination to complete any mission that is granted to them."
Guzman's recapture represents a major success in what has been an embarrassing ordeal for Mexico. For many, "El Chapo" has been a symbol of the Mexican government's ineptitude and corruption.
He has led one of the country's most powerful, violent drug cartels and escaped maximum-security prisons not once, but twice, the latest in July when he busted out through a hole into a mile-long tunnel and then on to freedom.
Last year's breakout spurred major criticism about the Mexican government's ability to safeguard such a notorious criminal, with some saying he should have been held in the United States.
U.S. officials were aware of the operation to capture Guzman, according to a law enforcement official.
The Americans provided assistance in the search, but his capture was the Mexican government's operation, the official said.
Mexican authorities were closing in on him for at least 24 hours before special forces moved in. The official said it's not a surprise El Chapo was located in Sinaloa.
"There was a belief he was in Sinaloa. That was his refuge. We would have been surprised if it were anywhere but Sinaloa," the official said.
Some U.S. officials were skeptical that Guzman would ever be captured again, especially alive, given the amount of protection he has in Mexico and his ability to escape prison twice, the official said.
The U.S. Justice Department previously sought extradition of El Chapo to the United States, and it is likely that the Justice Department will try to do so again.
U.S. Sen. John McCain urged such a transfer Friday when he tweeted, "Congratulations to the Mexican Navy on the capture of El Chapo. Now let's extradite him to the US."
The raid began after a citizen complained about armed people in a home, and when Mexican special forces went to the scene, they were fired upon by alleged members of organized crime, the Mexican navy said.
On Friday, Mexican authorities released a video of a person identified as Guzman, whose head was covered and who was being led by several armed officers from a vehicle to an airplane. Authorities released a video of a white structure where the raid occurred, and the footage showed several weapons.
In all, authorities seized four armored vehicles, eight rifles, a handgun, ammunition, and a tube rocket launcher with two charges, the navy said.
Led one of Mexico's richest, most violent cartels
Born in Badiraguato in Sinaloa state, Guzman started his career in the drug trade working for Miguel Angel Felix Gallardo, according to Time magazine in 2009.
He started his own cartel in 1980, expanding it into other states and even poaching some of his mentor's territory.
That creation -- the Sinaloa cartel -- soon became Mexico's most powerful and richest, a multibillion empire that supplied much of the marijuana, cocaine and heroin sold on American streets.
It was also one of the most violent. U.S. indictments claim the organization used assassins and hit squads to show its muscle.
The rivalry with other drug cartels has spurred an ongoing drug war that's left thousands of Mexicans dead.
"He's the epitome of the problem," Malcolm Beith, author of "The Last Narco," said of the man whose nickname translates as "Shorty." "He's a poor kid who had some family connections in the drug trade, no options, no real education ... (and) becomes a big-time drug lord."
Daring escapes create a legend
Authorities first caught up with Guzman in 1993 in Guatemala. He was extradited to Mexico and sent to the Puente Grande maximum-security prison following his conviction.
Yet even behind bars, Guzman lived like a king, Beith said. Eight years later he escaped via a laundry cart.
His legend grew as he evaded Mexican authorities, with stories of him helping the poor and paying everyone's tab at restaurants.
Singers in Mexico and the United States even hailed his exploits, with rapper Gucci Mane singing, "All I wanna be is El Chapo. And when I meet him I'mma tell him bravo."
But these exploits ended in 2014 with his arrest in a predawn operation on his beachside hideaway in the Mexican Pacific resort town of Mazatlan. Authorities found a shirtless Guzman, with an AK-47 next to his bed, and his beauty-queen wife in a no-frills condo tower.
Intense manhunt after latest escape
This time, Guzman was sent to Altiplano Federal Prison in Almoloya de Juarez. But he escaped in July, crawling through a hole in his cell block's shower area into a lighted, ventilated tunnel, then to a half-built house.
He then traveled north about 140 kilometers (85 miles) to San Juan del Rio, where two small planes were awaiting his arrival and took off from an airstrip, Attorney General Arely Gomez has said.
At the time, the Mexican President said he was "deeply troubled" by what he called "a very unfortunate event."
"This represents, without a doubt, an affront to the Mexican state," he said. "But also I am confident that the institutions of the Mexican state, particularly those in charge of public safety, are at the level, with the strength and determination, to recapture this criminal."
Since his escape, Guzman had been rumored to be many places, including as far away as Argentina. In October, authorities revealed they were hot on Guzman's trail, only to have him slip out of sight, though not before apparently breaking his leg.
Gomez said last fall that 34 people have been detained in connection with Guzman's breakout last year, including the drug lord's brother-in-law.