Flores Silva's capture comes two months after the military operation in which the cartel's leader, Nemesio Oseguera Cervantes, "El Mencho," was killed in the state of Jalisco.
The drug lord was arrested in the state of Nayarit during an operation carried out by special forces from Mexico's Secretariat of the Navy (SEMAR), Federal Security Secretary Omar García Harfuch said on his X account.
Flores Silva is originally from the western town of Huetamo, in the state of Michoacán. According to local media, he served as Oseguera Cervantes' security chief and later took over part of the CJNG's operations in the states of Nayarit, Jalisco, Zacatecas, Michoacán, and Guerrero, where he controlled several methamphetamine labs and oversaw the operation of various aircraft and clandestine airstrips for drug trafficking.
Some media outlets had suggested that Flores Silva could assume leadership of the CJNG following the death of "El Mencho."
The U.S. State Department had offered a $5 million reward for information leading to his location and capture.
Flores Silva was arrested in 2016 for his alleged involvement in an ambush against police officers in the town of Soyatlán, Jalisco, which occurred a year earlier, but he was later released.
Oseguera Cervantes died on February 22 during a Mexican Army operation in the town of Tapalpa, in southern Jalisco. His death triggered a wave of violence across some twenty states, leaving more than 70 people dead, including 25 members of the Mexican National Guard.