Omar Juarez was arrested in Saltillo, the capital of Coahuila, which borders Texas, the Los Angeles Times reported.
The Mexican navy said Juarez is in charge of Zetas operations in Saltillo.
Investigators said they hoped the arrest of Juarez would lead them to the Zetas' top leader, Miguel Angel Trevino, who took command last month after Heriberto Lazcano was killed in a shootout with navy special forces.
The Zetas are one of the largest cartels in Mexico.
Zetas operatives working with local police have been blamed for the death of the former governor's son in October.
Zetas members were involved in one of the largest Mexico prison breaks in September.
Officials say more than 55,000 people have been killed in drug-related violence in Mexico.
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