Archeologists used the spy boat as well as drones to find three shipwrecks on the Mediterranean seabed.
One of the shipwrecks dated back over 2,000 years and suggests there was a vast network of trade during the rise Ancient Greek cities such as Athens.
Ben Ballard, the team leader of the Ocean Exploration Trust (OET), said: “If our dates are correct, this is just as Alexander the Great is beginning his conquest.”
Alexander the Great, was a king of the Ancient Greek kingdom of Macedon and a member of the Argead dynasty.
The discovery follows Mr Ballard and his colleagues exploring the Eratosthenes seamount in expeditions backed by the OET in 2010 and 2012.
The technology used to scan the seamount included underwater drones and the OET’s Nautilus vessel which was originally a spy boat built by East Germany in the 1970s.
The team ended up finding two shipwrecks and 70 artifacts in 2010.
Mr Ballard is following in the footsteps of his father, Robert, who discovered the wreck of the Titanic.
News of the discovery has come after archaeologists earlier this year stumbled upon a lost city thought to have been founded by Alexander the Great.
Qalatga Darband in northern Iraq, believed to have been founded in 331 BBC, was discovered by a team of Iraqi and British archaeologists led by experts from the British Museum.
The city was found with the help of drones and declassified satellite photographs taken for military purposes.
John MacGinnis, the archaeologist leading the team in Iraq, told The Times: “It’s early days, but we think it would have been a bustling city on a road from Iraq to Iran.
“You can imagine people supplying wine to soldiers passing through.”
The site was first brought to the attention of archaeologists at the British Museum when the declassified CIA satellite photos from the 1960s were released.
The team then used drones equipped with a camera to discover the outlines of buildings hidden beneath fields of wheat and barley.