A son of Joaquin "El Chapo" Guzman, the infamous former boss of the Sinaloa cartel, pleaded not guilty to federal drug trafficking charges during an arraignment in Chicago federal court on Tuesday.

Joaquin Guzman Lopez, 38, appeared in an orange jumpsuit when entering his plea before U.S. District Judge Sharon Johnson Coleman, the Chicago Tribune reported.

Guzman Lopez, considered one of the lower-profile sons in the family, was arrested in El Paso, Texas, on Thursday with Ismael "El Mayo" Zambada Garcia, the top leader and co-founder of Mexico's Sinaloa cartel, after arriving aboard a private plane.

The arrests have prompted a swirl of international intrigue into how the elusive cartel leaders were captured. Zambada Garcia's Dallas-based attorney, Frank Perez, said in a statement following the arrests that Guzman Lopez kidnapped his client and forced him onto the plane.

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Sinaloa Cartel

Ismael "El Mayo" Zambada, a historic leader of Mexico’s Sinaloa cartel, left, and Joaquín Guzmán López, a son of Joaquin "El Chapo" Guzman, were arrested by U.S. authorities in Texas, the Justice Department said Thursday. (U.S. Department of State via AP)

A federal law enforcement source previously told Fox News that Guzmán López surrendered to U.S. authorities, but Zambada Garcia was captured. 

El Mayo

An undated police handout picture shows Ismael Zambada, known as "El Mayo." (Procuraduria General de la Republica/Handout via Reuters/File Photo)

Zambada Garcia and now-jailed drug lord "El Chapo" founded the Sinaloa cartel. 

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Zambada Garcia has been charged in numerous U.S. cases, including one filed in February in the Eastern District of New York accusing him of conspiring to manufacture and distribute fentanyl. Prosecutors said he led "one of the most violent and powerful drug trafficking organizations in the world."

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Now that Zambada Garcia is behind bars, experts say many powerful people in Mexico will be concerned that in a bid for a more comfortable deal, he could cooperate with U.S. authorities and accuse them of collaborating with the cartels.

Fox News' Adam Shaw and the Associated Press contributed to this report.