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The Loder Cup is awarded annually to encourage and honour New Zealanders who work to "investigate, promote, retain and cherish our indigenous flora".
Conservation Minister Kate Wilkinson announced the winner yesterday.
A professional plant ecologist for 30 years with the former DSIR and then Landcare Research, Dr Allen was pivotal in protecting thousands of hectares of native forest, shrublands, and coastal vegetation throughout Otago, Southland and the Kapiti Coast, she said.
His efforts had inspired others to cherish the native plants and ecosystems around them and he was instrumental in the establishment of several groups that promote the protection of indigenous vegetation, including Ecology Action Otago and the Otago branch of Beech Forests Action Committee.
Dr Allen was "the driving force" behind the efforts of the Otago Natural History Trust to establish Orokonui Ecosanctuary.
Nominated by the Otago Conservation Board, its chairwoman Abby Smith said Dr Allen's many contributions to the protection, cultivation and enjoyment of New Zealand's indigenous flora deserved recognition.
Dr Allen has published three books and more than 50 scientific papers.
He said the award was well-regarded within the botanical fraternity and he was honoured to be part of such a group.
"There's William Martin (winner 1960), Assoc Prof Alan Francis Mark (1975) and so many others. It's a fairly heady group."
He said he was grateful to the conservation board for nominating him, and "believing I was worth it".
Ms Wilkinson will award the Loder Cup to Dr Allen at a function later this year.