Victor Manuel Garcia Orozco, 47, is suspected of running criminal activities of the Jalisco New Generation cartel in the Cienega region, including drug smuggling, fuel theft and extortion, the interior ministry said.
He is also accused of involvement in "various attacks" against security forces, including the kidnapping and murder of two federal police officials in November 2013 in the neighboring state of Michoacan, the ministry said in a statement.
The investigation into their disappearance led to the discovery of 37 clandestine graves containing 75 bodies in the Jalisco municipality of La Barca, which borders Michoacan, the statement said.
Soldiers and federal police arrested Garcia Orozco on Wednesday in Tlajomulco de Zuniga, Jalisco, "without a shot fired" as he drove, the ministry said.
His arrest came days after federal police killed 42 New Generation suspects in what authorities described as an intense gunfight on a ranch at the Michoacan-Jalisco border on May 22. One officer was killed.
Between March and May, the cartel posed a major challenge to President Enrique Pena Nieto's security forces, killing around 30 police and troops, and downing a military helicopter, AFP reported.