The Mountaineering Council Of Scotland and the wild land charity the John Muir Trust had opposed the development of the Glenmorie wind farm to the west of the villages of Ardgay and Bonar Bridge, Sutherland.
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It had been reduced from 43 turbines, but the Highland Council had also objected.
Now Energy Minister Fergus Ewing has agreed with the findings of the Public Local Inquiry Reporter that the wind farm would cause unacceptable landscape and visual impacts, including on wild land.
Mr Ewing said: "The Scottish Government wants to see the right developments in the right places, and Scottish Planning Policy is clear the design and location of any wind farm should reflect the scale and character of the landscape and should be considered environmentally acceptable."
Lizzie Foot, project manager of Glenmorie Wind Farm LLP, said "Glenmorie could have contributed to Scotland's ambitious 100 per cent renewable electricity target and saved up to 112,000 tonnes of CO² per year, while providing a significant number of jobs for Highland firms. We are very disappointed this opportunity will not be realised."
Helen McDade, of the John Muir Trust, said: "This would have destroyed an area of wild land and had a damaging effect on peat land."
Meanwhile, an application to build a 18-turbine wind farm in the Borders has been referred by Mr Ewing for a Public Local Inquiry.
Scottish Borders Council had previously rejected consent for the Cloich Forest project on the grounds it would unacceptably harm the landscape.