Analysts say Jalisco New Generation could try to use him as leverage to win territory or other gains from what has been the country's dominant gang.
The Jalisco gang's power and reach have grown rapidly in recent years, often in direct competition with Guzmán's cartel, which has long been considered the strongest criminal organization in Mexico.
Earlier, officials had said they presumed that the kidnappers had taken another "El Chapo" son, Iván Archivaldo Guzmán.
Official sources have confirmed that Iván Archivaldo Guzmán is one of the people abducted by armed men.
The U.S. Treasury Department designated them as narcotics traffickers for their role aiding the cartel.
A group of six or seven people suspected to be members of Guzmán's Sinaloa Cartel were abducted by eight armed men from an upscale eatery in the heart of the resort early on Monday.
“The Sinaloa cartel operates here, we are a transit point," President of the Philippines Rodrigo Duterte said.
In February 2014 Heriberto Zazueta was indicted on drug trafficking and money laundering charges in the Northern District of Illinois.
The drug lord walked free in 2013 after a federal court overturned his 40-year sentence in agent Enrique "Kiki" Camarena's kidnapping, torture and murder.
Six Honduran National Police officers were charged Wednesday with conspiring with Fabio Lobo, son of former Honduran president Porfirio Lobo, to import drugs into the United States.