The suspect, Victor Manuel Perez Izquierdo, was in charge of kidnappings, extortion and killings for the Zetas in Quintana Roo state, a federal police statement said.
Police said information gleaned from the arrest of 10 other alleged Zeta members in Cancun last Saturday led to his capture Thursday. Perez Izquierdo was detained in Cancun while trying to escape in his car, the statement said.
While Quintana Roo has not seen the levels of violence plaguing Mexico's northern border states, it is a major drug trafficking zone.
Also Saturday, Guatemalan authorities said they captured 15 alleged Zeta members, five of them Mexican, for alleged links to the killing and dismemberment of a Guatemalan prosecutor.
Prosecutor General Claudia Paz y Paz said the suspects are under investigation in the death of local prosecutor Allan Stwolinski of Coban, a town about 120 miles northeast of Guatemala City. Authorities believe Stwolinski was slain in retaliation for helping seize 434 kilograms of cocaine from the Zetas.
Police seized a cache of weapons along with the 15 suspects, including eight rifles, two grenade launchers, a grenade and ammunition for an M-16 assault rifle, said Donald Gonzalez, spokesman for Guatemala's national police.
The alleged Zeta members were detained in Coban, a stronghold of the ruthless Mexico-based drug cartel near Guatemala's border with Mexico.
The suspects are also being investigated for a possible connection to the massacre of 27 cattle ranch workers in mid-May in another northern province plagued by drug cartels, Paz said.
Most of the workers were decapitated in the attack in Peten province near the Mexico border, in one of the worst massacres since the end of Guatemala's 36-year civil war. The owner of the ranch is being investigated for drug activity.
Guatemala is a major transshipment point for drugs, the U.S. State Department said in its latest narcotics report. The country's weak law enforcement, rampant corruption and proximity to Mexico have drawn Mexican drug cartels into its border regions.
Elsewhere in Central America, Honduran troops seized two tons of cocaine after an hour-long gunbattle with an estimated 60 drug traffickers, Defense Minister Marlon Pascua said.
The showdown took place in Raya, around 250 miles northeast of Tegucigalpa in the province of Gracias a Dios, bordering Nicaragua, Pascua said at a news conference.
"The drugs were transported in a four-motor boat," Pascua said. "We were unable to arrest any of the drug traffickers, who fled from the scene."
In the last month, Honduran police have seized more than five tons of drugs. According to authorities, 100 tons of cocaine pass through the country each year on their way from Colombia to the United States.