However the animals' welfare has been called into question, with spinal injuries and saddle sores being reported along with inhumane hours and lack of shelter in the 28 degree heats.
In response to this a new campaign 'In Their Hooves' has been launched to persuade tourists to take other modes of transport up the steep volcanic cliffs.
"Our In Their Hooves campaign aims to encourage tourists to stop and think before using donkey taxis to climb the steep steps at Fira port," said Catherine Rice, PR officer at The Donkey Sanctuary, which launched the initiative. "It suggests holidaymakers consider whether donkeys and mules are being treated humanely, have enough shade and water, as well as whether loads they are being asked to carry are suitable. If not, other options, such as walking or taking a cable car, might be a more responsible mode of transport."
Since 1979 there has been a cable car connecting the bay and the town, however many visitors still prefer to take a donkey.
Nikos Zorzos, the island's mayor told the Guardian that much of the tourism industry was aware of the problem ahead of the campaign launch:
"Representatives from the cruise liner association were here in my office this week promising to raise awareness [of the problem] and from our side we'll be distributing information leaflets. Our mules and donkeys are part of our tradition. Younger owners, especially, have understood that they need to be looked after."
There are about 4000 of the animals on the island.
The island deemed "any load exceeding 100kg" (including human cargo) to be cruel to the animals.
Breaking these animal welfare measures is punishable by fines of € 15000 ($25000) and up to a year in prison.
The move came after the animal welfare advocacy PETA raised 109,000 signatures for a petition titled: "Stop animal abuse of donkeys and horses in Santorini".
The island is a popular stop off on the itineraries of Mediterranean cruises.
Daily limits were put on ship disembarkations, to just 8000 visitors a day, down from 18000 in 2016 due to over-crowding.
Cruise passengers will now be asked to put themselves 'In their Hooves' as part of the new campaign, and the Cruise Lines International Association (Clia) took on board the new safeguarding measures for animal welfare.