Mario Cardenas Guillen, alias El Gordo, was arrested in the northern border state of Tamaulipas and taken to Mexico City where he was shown to the media, the Los Angeles Times reported Wednesday.
Navy spokesman Vice Adm. Jose Luis Vergara said he was found with a small amount of weaponry, cocaine, money and communications equipment.
Cardenas also faces charges in the United Sates, a spokesman for the Mexican federal attorney general's office said.
Cardenas is the brother of Osiel Cardenas Guillen, a long-time boss of the Gulf Cartel who was extradited to the United States in 2007.
A third brother, Antonio, died in a gun battle with Mexican marines in November 2010.
The Gulf Cartel once dominated the northeastern border region of Mexico. Recently, it has been battling its one-time ally the Zetas.