Rosalinda Gonzalez Valencia, the wife of Nemesio Oseguera Cervantes, alias "El Mencho," was taken into custody without incident Saturday night by Mexican navy agents in an affluent residential neighborhood, the newspaper Reforma said.
There was no immediate official confirmation of the arrest although the Interior Ministry called a news conference for Sunday that was expected to provide details on the development.
Officials cited by Reforma said Gonzalez, who was flown by helicopter to Mexico City after her arrest, managed the cartel's finances.
Sources in the Jalisco state prosecutor's office said security forces, civil defense and emergency medical services were put on alert in case of attacks by the cartel.
Mexican troops were deployed to guard approaches to the city, Mexico's second largest.
On Monday, Guadalajara was shaken by the attempted assassination of Jalisco Labor Secretary Luis Najera, a former state prosecutor who was attacked by armed men in a restaurant in central Guadalajara.
Assailants torched a passenger bus after the attack, killing an eight-month-old baby.
Najera suffered only minor injuries in the attack, but seven other people were more seriously wounded. One of the attackers was killed.
The Mexican government estimates that the Jalisco New Generation cartel has amassed a $50 billion fortune. It has a strong presence in nine Mexican states and connections with criminal organizations in the United States, Europe, Asia and Latin America.
In recent years, it has carried out attacks against military and police targets, including the 2015 downing of a military helicopter in which 20 soldiers and a policewoman were killed.
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