The deceased are both Finnish citizens - a 25-year-old woman and a 21-year-old man.
According to Estonian police, the first body was discovered at 3:00 a.m. and the second at 5:00 a.m. The police said that the incidents did not appear to be related and neither case indicated there had been any violence involved.
The bodies of the deceased passengers have been sent for an autopsy in order to determine the cause of death.
Estonian police said the deceased had spent the night in their staterooms onboard the ship while it was docked at the port of Tallinn. The cabins were not situated close to each other on the ferry.
The bodies were both discovered by fellow passengers. An Estonian police patrol and an ambulance were called to the scene.
For other Silja Europa cruiseferry accidents see at the ship's CruiseMinus page.