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.
Initially the most affected communities were Arroyo Seco, La Tuna and La Palma, but violence soon spread to Huixiopa, La Vainilla and San José del Llano.
The drug lord was flown to Mexico City late Wednesday and then transported to the Altiplano prison outside the capital, the same prison that Sinaloa Cartel leader Joaquín "El Chapo" Guzmán escaped from in 2015.