The official told the Los Angeles Times Guzman was nabbed in Mazatlan overnight and whisked away to Mexico City.
It was not known if U.S. drug agents played a role. The Times said the operation was based on a tip from an informant and Guzman was arrested without putting up a fight.
Mazatlan is the capital of the Mexican state of Sinaloa, the namesake of the long-running smuggling ring that has moved tons of marijuana and cocaine into the United States.
Guzman, known as "El Chapo," had been a wanted fugitive in Mexico since breaking out of a Mexican prison. He had been originally arrested in the 1990s.
The Times said the arrest came after a series of raids by the Mexican military on locations in Sinaloa owned by Guzman associates.
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