The corpse of Heriberto Lazcano, founder of the brutal Los Zetas gang, was being stored by the authorities at a funeral parlor in northern Mexico.
The Mexican Navy said tests confirmed that the man killed was Heriberto Lazcano.
Infamous for mass killings, the Zetas control key drug-trafficking routes in north-eastern Mexico.
Heriberto Lazcano, also known as “the executioner”, was killed in a gun battle with marines on Sunday in Progreso, some 125 km (80 miles) west of the Texan border in Coahuila state, the navy said.
His identity had not been confirmed until now.
The Navy said that fingerprints taken from the body matched those on its database, and that photos of the corpse’s face were compared with previous photographs of Heriberto Lazcano.
The Navy said that the body had then been handed over to the local authorities in Coahuila.
But early on Monday, a group of armed men raided the funeral parlor where the body was being kept, and stole the corpse, attorney general Homero Ramos told a news conference.
Heriberto Lazcano is suspected of involvement in hundreds of killings, including that of crusading newspaper editor Francisco Ortiz Franco in 2004.
The US had put up a $5 million reward and Mexico another $2.3 million for information leading to Heriberto Lazcano’s capture.
Mexican police believe a recent surge in mass killings is due to a split within the Zetas cartel.
Heriberto Lazcano was thought to be the leader of one faction, while the other is led by Miguel Angel Trevino Morales.
In the nearly six years of Felipe Calderon’s presidency, more than 50,000 people are believed to have died in violence blamed on organized crime.
The navy has been at the forefront of operations against Mexico’s drug cartels.
On Monday, it said it had arrested suspected regional Zetas leader, Salvador Alfonso Martinez Escobedo, who the navy says was behind the 2010 murder of 72 migrants in northern Tamaulipas state.
Officials say Escobedo works for Trevino Morales.
Trevino Morales, known as Z40, has a reputation for equal if not greater brutality than Heriberto Lazcano and remains at large.
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