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Organisers posted notice of the cancellation to social media this morning.
"Due to the ongoing restrictions under Alert Level 2, it is with heavy hearts and deep regret that the Emerson’s Dunedin Marathon is cancelled," the post said.
"This was a difficult decision and we feel deeply for our loyal participants who have trained long and hard for this year's event."
The safety of participants, volunteers and supporters was paramount and the organising committee had worked tirelessly through every scenario to have the marathon happen, it said.
All entries from this year would automatically roll over to the 2022 event, which was planned for September 11.
"However, if you find you are unable to take part in the 2022 event, a 75% refund can be claimed by contacting: firstname.lastname@example.org"
Planning for next year had already begun.
Last year's marathon was also cancelled - for the first time in its history - because of uncertainties caused by Covid-19.