It's unclear how the gunmen grabbed him, as no shots were fired in the raid. Authorities said nine female companions of the victims were not taken by the kidnappers.
Officials said earlier today that they believed the older Guzmán son, Iván Archivaldo, had been taken captive, but Almaguer said authorities now believe it was younger sibling Jesús Alfredo.
Both are viewed in Mexico as "narcojuniors," aspiring drug lords brought up in a luxury world of guns and cash.
Guzmán Salazar's kidnapping is the latest setback to his father's hopes of keeping rivals at bay and the family business running from behind bars.
In June, a large convoy of drug commandos attacked his tiny home town of La Tuna in the Sierra Madre, forcing their way into the house of the kingpin's elderly mother. They shot up the town's highway sign and torched several homes and vehicles, though 86-year-old Consuelo Loera de Guzmán was reportedly unharmed.
Mexican news reports attributed the raid to upstart gangster Alfredo Beltrán Guzmán, 24, aka "El Mochomito" (the Little Desert Ant). He is the son of Alfredo Beltrán Leyva (the Desert Ant), a former business partner of Joaquín Guzmán's turned mortal enemy, who blames his 2008 arrest on a betrayal by Guzmán.
It's a blood feud, literally: The Little Desert Ant and El Chapo are cousins.
The Beltrán Leyva clan has battled the Sinaloa cartel for dominance of the lucrative drug trade in Mexico's western Sierra Madre ever since. In 2008, Gúzman's 22-year-old son Edgar was killed in a hit blamed on Beltrán Leyva gunmen in the parking lot of a tyre shop in the Sinaloa capital of Culiacan.
The Guzmáns have a long list of enemies, but authorities hinted today that the kidnapping was believed to be carried out by the Jalisco-based New Generation cartel that is challenging the Sinaloa organisation for supremacy along Mexico's Pacific coast smuggling routes.
Joaquín Guzmán, who has escaped twice from Mexico's toughest prisons, is locked up at a facility just south of the US border. His lawyers claim he has been the victim of "cruel and unusual punishment" from prison authorities, who allegedly keep him in solitary confinement and interfere with his sleep.
Guzmán faces a slew of drug trafficking charges in several US federal courts. Mexico's Foreign Ministry has given the green light to his extradition, but Guzmán's legal team is fighting his transfer across the border.
According to Guzmán's lead lawyer, the world's most notorious drug lord has been "depressed". But Mexican officials insist that his health is fine.
