The suspect, who was not identified by name, was captured in the Sinaloa state capital of Culiacan and will be presented to the media Monday morning, the army said.
Guzman, Mexico's top drug lord, is one of the world's richest men, and has eluded authorities by moving around and hiding since his 2001 escape from prison in a laundry truck.
The army said the man they had arrested also ran cartel activities in Durango and southern Chihuahua state, and was responsible for carrying out secret burials of cartel victims, kidnapping, extortion and arson. They did not say if the arrest moved the military closer to capturing Guzman, an arrest that would be seen as a major victory for the government of President Felipe Calderon.
Guzman is worth more than $1 billion, according to Forbes magazine, which has listed him among the "World's Most Powerful People." He has a $7 million bounty on his head, and thousands of law enforcement agents from the U.S. and other countries working on capturing him.
His cartel controls cocaine trafficking on the Mexican border with California and has moved eastward to the corridor between the Mexican state of Sonora, which borders Arizona.
Separately, Mexican soldiers discovered 13 bodies in an abandoned truck Sunday along with a message that they were killed in a war between rival drug cartels in the eastern state of Veracruz, officials said.
The bodies were found in Tamaulipas state, a few hundred yards (meters) from its border with Veracruz, according to the Tamaulipas attorney general's office. The office said that 10 of the bodies had been decapitated.
The area has been the scene of bloody battles between the Gulf and Zetas cartels, and a pair of banners alluding to a rivalry were found in the truck, the statement from the attorney-general's office said.
On Friday, the attorney general's office in Veracruz said it had found 10 bodies in a different area along the border with Tamaulipas after receiving a tip.
On Thursday, three U.S. citizens traveling to spend the holidays with their relatives in Mexico were among those killed in a spree of shooting attacks on buses. In the spree, a group of gunmen attacked three buses in Veracruz, killing a total of seven passengers.
The Americans killed were a mother and her two daughters who were returning to visit relatives in the region.
The five gunmen who allegedly carried out the attacks were later shot to death by soldiers.
Earlier, the gunmen also killed four people in the nearby town of El Higo, Veracruz.
Local police in Veracruz have become so corrupt that on Wednesday the government decided to dissolve the entire force in the state's largest city, also known as Veracruz, and sent the Navy in to patrol. Some 800 police officers and 300 administrative employees were laid off.
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