The kingpin had been on the run since absconding from jail six months ago.
The news of his re-arrest was broken by Mexican President Enrique Pena Nieto who tweeted: “Mission accomplished: we got him.”
It has been reported that El Chapo, born Joaquin Guzman, was seized after a shoot-out with Mexican marines near his home state in north Mexico.
Chapo broke free from jail for a second time (he escaped from prison in 2001 and was re-arrested in 2014) in July resulting in a worldwide manhunt.
He escaped the maximum-security jail via a 1.5km (mile) long tunnel dug in the showers.
The US government had offered a $5million reward for any information that lead to his capture.
The 57-year-old is the leader of the Sinaloa cartel who have been responsible for smuggling cocaine, heroin and methamphetamines into the US.
He is reportedly worth $1bn.