The animal, which is unique to its island home and is larger than the common vole found elsewhere in Britain, came from Belgium more than 5000 years ago.
A team of scientists, led by Aberdeen University and Cornell University in the US, has been working on the Orkney vole's genealogy. The findings give an unprecedented insight into the zoology of prehistoric Europe.
The scientists discovered European common voles were likely to have been brought to Orkney by farmers from the coast of Belgium as early as 5100 years ago.
Professor Keith Dobney, of Aberdeen University's archaeology department, is one of the co-directors of the research. He said: "The Orkney vole, a sub-species of the European common vole, is found nowhere else in mainland or island UK. Yet the extensive archaeological record from Orkney has produced thousands of their bones and teeth, suggesting they most likely arrived with early farmers or through Neolithic maritime trade and exchange networks.
"Where in Europe they came from and when they were introduced has been a mystery for decades, but new genetic techniques and direct dating of their bones have finally allowed us to answer these questions."
The study was one of the largest of its kind, and its results were published in Molecular Ecology.
The research team used a combination of DNA analysis and morphological techniques, studying the form and structure of organisms to provide an understanding of the creature's origins and, by association, an insight into the Neolithic culture of Orkney.
Dr Natalia Martinkova, of the Academy of Sciences in the Czech Republic, carried out the genetic studies on living common voles from continental Europe and Orkney. She said: "Although our modern DNA results did not reveal exact genetic matches with any populations we sampled across continental Europe, the closest were from populations living today on the coast of Belgium, the likely origin for the original Orkney populations."
By taking voles to Orkney, Neolithic traders and settlers unwittingly became early conservationists: the genetic signature of the common vole in mainland Europe has changed dramatically, but its Orcadian cousin shows how voles would have been more than five millenniums ago.
Professor Jeremy Searle, co-director of the research from Cornell University, said: "The genetic variation in all western continental European common voles was shown to be much less diverse than those modern populations on the Orkney Islands - completely the reverse of what would be expected for a normal/traditional model of island colonisation and evolutionary history.
"This most likely suggests what we have on Orkney is a snapshot of the original genetic diversity of common voles that existed in continental Europe in prehistory; a diversity that has since been lost from the European mainland but not from Orkney."