Felipe Viveros Garcia, 30, was detained in the western state of Jalisco along with two other suspects, Jose Bernabe Lopez Alcaraz, 43, and Froylan Barrera Morales, 40, the national security commission said in a statement.
The three men are accused of taking part in organized crime, murder, kidnapping, extortion and gun smuggling. The statement did not say when they were captured.
Viveros Garcia operated in several towns in the states of Guerrero and Jalisco, the commission said, adding that as well as the more than 200 murders he is "linked to at least 10 documented kidnapping cases" and accused of demanding extortion payments from state authorities in Jalisco.
More than 77,000 people have died in drug cartel-related violence in Mexico over the past seven years.
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President Enrique Pena Nieto, who took office a year ago, has pledged to reduce the murders and kidnappings plaguing his country, but while homicides are down, abductions have soared.
This past month, authorities unearthed 64 bodies in mass graves in a region of Jalisco bordering the state of Michoacan. The two states are in the throes of a turf war between the Jalisco New Generation cartel and Michoacan's Knights Templar gang.
Officials in Guerrero said yesterday that they had found the dismembered bodies of eight family members who had been kidnapped.
The victims ranged in age from 18 to 40. They were abducted Thursday by gunmen in the town of Teloloapan.
The bodies were found Friday in plastic bags dumped along a highway. The remains showed signs of torture and gunshot wounds, a Guerrero state government statement said.