Duncan MacDougall and Przemek Krawczyk were on board the Nancy Glen when it capsized in Loch Fyne in Argyll and Bute on January 18.
The alarm was raised by a third fisherman who was pulled from the water by the crew of a passing boat.
A specialist lifting barge brought the vessel to the surface on Thursday and two bodies were recovered.
They have now been formally identified as those of the missing men.
A Crown Office spokesman said: “The Crown’s Scottish Fatalities Investigation Unit have completed the formal identification process following the recovery of two bodies from the Nancy Glen boat which sank in Loch Fyne in January 2018.
“It can now be confirmed that the bodies are those of the two missing crewmen, Duncan MacDougall and Przemek Krawczyk.
“The families have been informed and the bodies have been released to them.”
A mandatory Fatal Accident Inquiry will be held as the deaths occurred at a place of work, however it is not yet known when it will take place.
A major search was launched by police and the coastguard after the boat sank in January, but no trace was found of the missing men.
The Marine Accident Investigation Branch (MAIB) previously conducted a seabed survey of the ship which was said to be lying at a depth of more than 459ft (140 metres).
The MAIB said it could not raise the boat but the Scottish Government stepped in to work with salvage specialists and the families of the crewmen to support efforts to retrieve the bodies.