The 24-year-old man left his three-year-old son with his mother to run an errand in November 1998, just before he disappeared, local media reported on Monday.
A murder investigation was launched at the time, for various reasons the police would not reveal, but a body was never found and no arrests were made.
Bones found in a plastic bag on a farm near Hörby, southern Sweden, last month have now been identified as belonging to the man. The grim discovery was made by a worker sent out to drain sludge from the well.
Police named him as Jacob Tillman, from the Höganäs area of southern Sweden. His family had been informed, they said.
Officers were able to determine the identity of the remains through dental analysis and an autopsy appeared to confirm their initial suspicions that he was killed.
“An autopsy of the body indicates that Jacob's life was taken by another person and the crime is being investigated as murder. Police have been investigating Jacob Tillman's disappearance as murder since 1999 due to information obtained during the probe,” read a police statement published online.
The Hörby farm had been abandoned since 2011 when the previous owner moved out. A Malmö-based couple bought it in November 2014 and eventually started to clear scrap and waste from the yard, including from the well where the skeleton was found.
“It was about 160 centimetres tall and had the shape of a human. I would like to think it's an animal but unfortunately it probably isn't. It looks too much like a body,” the worker who found the skeleton, Peter Åhlin, told the Aftonbladet tabloid in August.