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 is also believed to have been involved in the gunning down of rival boss Domenico Bonarrigo in a clan war. Bonarrigo's men got revenge by feeding the suspected gunman, Ferraro ally Francesco Raccosta, alive to pigs in 2013.
Maropati was founded in the first century after being used as a hideout by people fleeing Saracen pirates on the coast.
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"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 said.
Police raiding the bunker found a submachine gun as well as a collection of rifles and pistols hung on the wall.
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.