The Interior Ministry said federal police arrested Ines Coronel Barrera, 45, Tuesday in the border state of Sonora, the Los Angeles Times reported.
Coronel is the father of Emma Coronel, wife of Mexican drug lord and fugitive Joaquin "Chapo" Guzman. Authorities said they consider Coronel to be a key player in Guzman's empire.
The ministry said federal police also confiscated marijuana officials said was bound for Arizona, weapons, vehicles and four people presumed to be bodyguards.
In January, Coronel was added to the U.S. Treasury Department's so-called kingpin blacklist, the Times said. The Treasury Department called him a major marijuana trafficker and banned U.S. companies, banks and individuals from conducting business with him.
Eduardo Sanchez, the Interior Ministry spokesman who announced Tuesday's capture, cited several Mexican government agencies that worked "in close coordination with each other" to begin bringing Coronel to justice and "contribute to a Mexico in peace."
The arrest, the first under new President Enrique Pena Nieto, comes as Mexico begins trying to reduce the level of involvement of the United States in Mexico's drug war.
The Times reported officials in the Nieto administration were concerned upon learning how deeply involved U.S. advisers were in areas of security and law enforcement during the administration of President Felipe Calderon.
U.S. President Barack Obama travels to Mexico this week. During a news conference Tuesday in Washington, Obama said would wait until he speaks with Nieto Thursday "to see exactly what are they trying to accomplish" and how the shift will alter the U.S.-Mexico relationship.