The body of the 67 year old Glenswilly man was found in the bathroom of his home at Drumacancoo in the early hours of Sunday morning last.
At first it was thought that Mr Doherty’s death had been down to natural causes or perhaps suicide.
Supt Eugene McGovern of Milford Garda Station confirmed the investigation has been upgraded to a murder investigation but said he could not say how he died.
“As a result of post mortem our enquiries have been upgraded to a murder enquiry.
“We are not releasing circumstances of death but we can confirm he suffered a traumatic death and we are satisfied to upgrade the death to a murder investigation,” he told donegaldaily.com at Letterkenny Garda Station where the murder inquiry is based.
The father of four was well-known around the area.
He was a retired farmer who had a major interest in horses.
Mr Doherty was known to the Gardai and had convictions for various public order offences.
He was last seen in Letterkenny on Saturday afternoon and now Gardai want to trace his movements before he arrived home that evening.
Garda forensic experts continue to carry out an investigation around Mr Doherty’s home which remains sealed off.
A full incident room has been set up at Letterkenny Garda station.