Mexican marines and the police, aided by information from the United States Drug Enforcement Administration, immigration and customs officials and the United States Marshals Service, took him into custody without firing a shot, according to Mexican officials.

Mexico’s attorney general, Jesús Murillo Karam, said a later forensic exam made it “100 percent” certain the man was Mr. Guzmán; the tests were done to avoid the kind of embarrassment Mexican officials faced in June 2012 when they announced the arrest of Mr. Guzmán’s son, only to later discover it was not him.

Mr. Guzmán faces a slew of drug trafficking and organized crime charges in the United States, which had offered $5 million for information leading to his arrest in the hopes of dealing a crippling blow to an organization that is the country’s top provider of illicit drugs.

Mr. Guzmán’s Sinaloa Cartel is considered the largest and most powerful trafficking organization in the world, with a reach as far as Europe and Asia, and has been a main combatant in a spasm of violence that has left tens of thousands dead in Mexico.