The bodies were found during preparatory work to raise the fishing boat after an ambitious salvage operation began on May 9th with the hope of raising the wreck and identifying the remaining victims.
The two bodies have been placed on board the Italian Navy ship Tremiti, which is overseeing the operation.
An estimated 800 people died when the small fishing boat sank in April 2015, in what is thought to be the single greatest disaster of Europe's ongoing migrant crisis. There were just 28 survivors.
So far, just 171 bodies have been found near the wreck, with the Italian authorities suspecting some 600 migrant corpses lie trapped in the ships hull.
Before the navy began lifting the wreck at 6pm on Wednesday evening, external parts of the ship had been cut away, all entrances and exits sealed and a net placed over the ships hull.
A video taken during preparatory work can be seen below.
“Given the depth of the wreck, [which lies at a depth of 370 meters] the entire process is robotized,” Egidio Ibba of Impresub – the Italian company who designed a special robotic module for the coastguard told Corriere.
“The robotic module was hooked over the boat, gripping it with a hydraulic arm, the module can now be pulled to the surface, Ibba added.
It is expected to take 25 hours to raise the wreck.
Assuming weather conditions are favorable, the ship will then be placed on a barge and towed to the Melilli Nato base in Augusta, Sicily.
Once ashore, forensic scientists will take DNA samples and carefully collect and catalogue identifiable features from the hull's heartbreaking cargo, in the hope the victims can one day be identified.