The bodies were found near the grounds of the Castle Hotel last Thursday.
Historic monuments group Cadw suggests building foundations also dating back to medieval times have been found at the site.
Archaeology Wales are carrying out further excavations in the hope of finding more human remains.
History lecturer Dr David Craik believes the bodies possibly date from the Wars of the Roses as the castle was almost constantly under siege from 1461 to 1468, according to the Cambrian News.
Dr Craik, who is also president of the Harlech Historical Society, said: “The discovery of the burials at Harlech Castle is the most exciting archaeological find since the discovery of a gold torque in 1922.”