Giuseppe Ferraro, 47, and Giuseppe Crea, 37, both high-ranking members of the powerful and immensely wealthy 'Ndrangheta organised crime group, had been on Italy's most dangerous fugitives list, police told AFP.
Ferraro, found guilty in absentia of a string of brutal murders and described as “extremely dangerous” by the police, had been on the run for 18 years.
Crea, wanted for mafia association and extortion, disappeared 10 years ago.
Ferraro's clan is also believed to have been involved in the gunning down of rival boss Domenico Bonarrigo in a turf war.
Bonarrigo's men got revenge by feeding the suspected gunman, Ferraro ally Francesco Raccosta, alive to pigs in 2013.
The bunker contained an impressive arsenal of weapons .Photo: Polizia di Stato
“They were living in a concrete bunker hidden by dense bushes and trees,” said prosecutor Federico Cafiero De Raho, describing the hideout in the mountains near the town of Maropati in the Reggio Calabria region of southern Italy.
Maropati was founded in the 10th century after being used as a hideout by people fleeing Saracen pirates on the coast.
“They were living like animals, a cold life cut off from society,” but with enough contact with the underworld to rule on gang matters when necessary, Cafiero De Raho told a press conference.
Police raiding the bunker found a submachine gun as well as a collection of rifles and pistols hung on the wall.
Killer 'known to Vatican spy'
The men were “still actively managing the clan's affairs and had a military control over the territory,” said Rosy Bindi, head of the parliamentary anti-mafia commission.
Crea is suspected of having gunned down Francesco Inzitari, the teenage son of a rival, in 2009.
The murder returned to the headlines in 2014 after Italy's L'Espresso magazine claimed that Inzitari's killer was known to a local priest who worked as a spy for the Vatican's secret services.
“Now that the territory has been freed of these two dangerous fugitives, I invite people to come forward and collaborate to throw light on their crimes, like the murder of Francesco Inzitari,” Cafiero de Raho said.
Photographs released by the police showed one of the men in a black jumper and brown fleece in the moment of his arrest, with boxes of cherry tomatoes and a flask visible next to the kitchen sink behind him.
Life had become increasingly difficult for the pair since June last year, when a police crackdown severely weakened the network of clan members helping them survive in the woods, investigators said.
The 'Ndrangheta is credited with controlling much of the world's cocaine trade and police describe the group as the most active, richest and most powerful syndicate in Europe.
“Today is another great day for the country, because today justice once again has won, and done so impressively,” Italy's Justice Minister Angelino Alfano said in a statement.