The remains — which had teeth in good condition — were found in two graves that date to between 675 and 650 B.C., Agence France-Presse reported. They rest in an ancient cemetery where the National Library of Greece and the National Opera are being constructed.
The men were lined up in the graves, and the hands of 36 of them were tied with iron shackles, AFP reported.
The finding could illuminate an important chapter in Greek history.
Cylon lived during the 7th century B.C. He came from a noble family in Athens and became somewhat of a star after winning the double footrace at the Olympic Games.
So he wanted to seize upon his celebrity status. With some help from his tyrant father-in-law, he attracted a band of followers to take the Acropolis.
But they were besieged for quite some time. After claiming the protection of the goddess Athena, they relented only after nobles in charge promised to spare their lives.
Cylon and his brother managed to escape, according to Athenian historian Thucydides. The band of followers remained with no food. Guards eventually convinced them that they could leave safely but "then led them away and put them to death," Thucydides wrote.
"They even slew some of them in the very presence of the awful Goddesses at whose altars, in passing by, they had sought refuge," according to Thucydides. "The murderers and their descendants are held to be accursed, and offenders against the Goddess."
The episode — dubbed the Cylon Conspiracy, and also described by ancient Greek historian Plutarch — damaged the reputation of the ruling aristocratic family for hundreds of years.
Archaeologists haven't confirmed that the remains belong to men from that band of followers; regional archaeological services director Stella Chryssoulaki described the theory on Thursday, according to AFP.
Greece's Central Archaeological Council said in a statement that it will further investigate the remains given "the high importance of these discoveries."