Edinburgh University researchers found Japanese sika deer, brought to the country in the 19th Century, have bred extensively with native red deer.
In some areas as many as 40% of deer are of mixed breed.
Such cross-breeding could alter wild deer in Scotland permanently.
Research by academics at St Andrews University suggests that large numbers of Japanese sika deer are interbreeding with red deer, creating a hybrid which could see the end of the native species within 50 years.
The study was conducted in Kintyre and is in the journal Molecular Ecology.
Although it was already known that sika cross-breed with red deer, it was thought the overall impact on the native species was low.
Helen Senn, of the university’s school of biological sciences, said: “The extent of cross-breeding we uncovered is worrying, and suggests that similar populations of red-sika hybrids could exist undetected elsewhere in the UK.”
“This cross-breeding represents a serious threat to wild red deer on mainland Scotland.”
“Thankfully legislation already exists to protect the red deer on many of the Scottish islands from cross-breeding with sika deer but the mainland red deer remain at risk.”
The research was funded by the Natural Environment Research Council and the Macaulay Institute.