Omar Trevino Morales, known as Z-42, was arrested on March 4 in the city of Monterrey in the northern state of Nuevo Leon, police said.
Z-42 is said to have run the cartel since the 2013 arrest of his brother, Miguel.
The arrest comes days after Mexican police captured another suspected drug lord, Servando “La Tuta” Gomez.
Servando Gomez was the leader of the Knights Templar cartel in Michoacan state.
Omar Trevino Morales is wanted in the US and Mexico on charges of drug trafficking, kidnap and murder.
Mexican media, citing officials, said he had been seized in the Monterrey suburb of San Pedro Garza Garcia in a joint operation by the army and the federal police.
The Zetas cartel is believed to be behind some of the bloodiest crimes carried out by Mexico’s drugs gangs.
It was blamed for an arson attack on a Monterrey casino in 2011 that killed 52 people and for dumping 48 decapitated bodies near the city in 2012.
Analysts say the cartel was weakened by the killing of former leader Heriberto Lazcano in 2012 and the capture of Miguel Angel Trevino Morales in 2013.
The Zetas began in the 1990s as the enforcement arm of another powerful criminal gang, the Gulf Cartel.
They were made up of defectors from an elite military unit and quickly became known for their brutality.
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