Another organization tracing its origins back to the Guadalajara OCG is the Arellano Félix organization (AFO) also known as the Tijuana OCG. The group is named after the Arellano Félix brothers (seven in all, five involved in drug trafficking) who are the nephews of the Guadalajara OCGs founder Miguel Angel Félix Gallardo. A rival to the Sinaloa organization when the Guadalajara organization broke up, the AFO was at one time allied with the Gulf OCG.

Since 2002, the AFO leadership has suffered serious losses including the death the group's leader, Ramon Arellano-Felix, killed in a shootout with police forces. Shortly thereafter, Ramon's older brother, Benjamin Arellano-Felix, was arrested.

On August 16, 2006, the U.S. DEA and Coast Guard arrested AFO member Francisco Javier Arellano Felix off the coast of Mexico. He was charged with money laundering and running a criminal enterprise. After pleading guilty, he was sentenced to life in prison without the possibility of parole in the United States. Additionally,
Javier's brother, Francisco Rafael Arellano Felix, was extradited to the U.S. in September 2006, and sentenced to six years imprisonment in late 2007. Mexico also sentenced Benjamin Arellano Felix to 22 years in prison for a myriad of charges related to organized crime and illicit activities. The last brother, Eduardo "El Doctor" Arellano Felix, wanted by the U.S. on charges of narcotics smuggling and money laundering, was arrested in Oct 2008.

The AFO was responsible for supplying an estimated 40 percent of the cocaine consumed within the United States during its heyday. In 2008, it was reported that the AFO continued to operate in 15 Mexican states with its principal base of operations located in Tijuana.

After the arrest of Eduardo Arellano Felix in 2007, a power struggle emerged within the cartel between Fernando "El Ingeniero" Sanchez Arellano and Eduardo Teodoro "El Teo" Garcia Simental. As a result, Teodoro Garcia left the organization and created his own gang, which is rumored to be aligned with the Sinaloa OCG. Teodoro Garcia and his faction became rivals of Fernando Sanchez Arellano and the remnants of the Tijuana OCG. The increase in violence in Baja California has been attributed in large part to the rivalry between "El Teo" and his former associates.

The atrocities committed by "El Teo" made him one of Mexico's most-wanted, with a $2.1 million USD reward for information leading to his arrest. On January 12, 2010, Mexican authorities were successful in capturing the drug kingpin.