Judges praised the business, which has grown from a 16-bedroom guest house in 1988 to a resort comprising two hotels with 64 bedrooms, for its year round occupancy of around 90%.
Owned by the Johnston family for 27 years, Auchrannie today offers 30 self-catering luxury lodges, three restaurants, a shop, two leisure clubs with pools, a spa, outdoor adventure centre and a children's play barn.
The award was presented at a celebratory dinner for 500 guests last night at the Crowne Plaza, Glasgow.
Damian Riley-Smith, managing director of Paragraph Publishing, publisher of Scotland Magazine and the awards' organiser, described Auchrannie as "an inspiring Scottish tourism success story".
Judging of the annual awards involves three months of mystery visits across Scotland's hotels.
Alongside Auchrannie, other key winners included Robert and Vivien Kyle, owners of the Lochside Hotel & Spa, Ayrshire, who were named Scottish Independent Hoteliers of the Year.
Jamie Stevens of Glasgow's Hilton Garden Inn was voted Scottish Hotel Manager of the Year. He was recently appointed to head up the new Urban Village Resort which opens in July in Glasgow.
Chef of Year was Tony Sarton of Twenty Princes Street at Edinburgh's Royal British Hotel, which is shortly to be re-branded as the boutique Hotel Indigo.