A control zone has been set up and beekeepers have been warned to be on alert following an outbreak of American Foulbrood.
The infected single hive, near Bridge of Earn in Perthshire, was detected by the beekeeper.
The fatal bacterial disease, which targets honeybees, was confirmed by Science and Advice for Scottish Agriculture (SASA) on Wednesday.
The Scottish government said it is the first finding of AFB in Scotland this year.
In 2022, 10 honeybee colonies from seven different apiaries tested positive for AFB.
AFB is a notifiable disease under The Bee Diseases and Pests Control (Scotland) Order 2007.
As there is no permitted treatment in the UK, infected hives are destroyed to curb its spread.
Beekeepers within 3km from the affected colony will be alerted via BeeBase and have been encouraged to increase their biosecurity.
Sheila Voas, chief veterinary officer for Scotland, said: “The finding of AFB is a timely reminder that beekeepers should remain vigilant for signs of the disease at all times.
“There are no risks to public health and no implications for the quality and safety of Scottish honey.
“The movement of bees and related equipment into, or out of, the affected apiary will be under specific controls supervised by Scottish government bee inspectors and will include enhanced biosecurity measures and increased vigilance in the area.”
Ms Voas added: “Beekeepers should make sure they are aware of the symptoms of AFB and report suspicion of disease to the Scottish government bee health team.
“I would also encourage Scottish beekeepers to register on BeeBase so that they can be informed of any disease outbreaks in their area.”