The Mexican drug lord was paraded before cameras before being bundled into a helicopter to Altiplano prison in central Mexico.
El Chapo (Shorty) Guzman escaped from there in July through a tunnel dug in the showers.
He was arrested on January 8 in the city of Los Mochis in his home state of Sinaloa – which he had come to dominate through the drugs cartel he led.
During the early-morning raid, El Chapo Guzman managed to flee through a drain but was later caught by marines in a shootout.
Six people, including one marine, are reported to have been killed.
Part of the reason El Chapo Guzman was tracked down was because he contacted actors and producers in the hope of making a movie about his life, Mexico’s Attorney General Arely Gomez said.
Mexican President Enrique Pena Nieto described Joaquin Guzman’s arrest as a “victory for the rule of law”.
The United States congratulated the Mexican government but did not indicate whether prosecutors would seek Joaquin Guzman’s extradition.
In a statement, Attorney General Loretta Lynch said Joaquin Guzman had caused “significant violence, suffering and corruption on multiple continents”.
El Chapo Guzman’s July escape was his second – he was first arrested in Guatemala in 1993 and escaped from Puente Grande jail in 2001, reportedly in a laundry basket after bribing officials. He was on the run for 13 years before being held again in 2014.
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