A member of the Otago anatomy department in 2009, she has pioneered the use of evolutionary genetics to trace Pacific migrations.
The university awards the medal for outstanding scholarly achievement, including the discovery and dissemination of new knowledge.
Prof Matisoo-Smith was shocked, yet thrilled, to receive the honour.
And she felt a bit awkward being singled out as an individual researcher since all of her work is collaborative and cross-disciplinary.
She worked closely with colleagues in the anthropology and archaeology department and in several other Otago departments, as well as with postgraduate students in the anatomy department.
An engagement with and by communities across the country and the Pacific was "essential to the research''.
Receiving this medal was "a big 'thumbs up'" to multidisciplinary research that engaged with the general public and she shared the award with "my many collaborators and students'', she added.
Prof Matisoo-Smith and her research group have worked closely with the Rangitane o Wairau iwi to undertake the first analysis of ancient mitochondrial human genomes from the Pacific.
The individuals studied were from the archaeological site of the Wairau Bar, thought to have been one of the first places settled in New Zealand.
Announcing the honour, Otago vice-chancellor Prof Harlene Hayne said Prof Matisoo-Smith had "reshaped our understanding of the last great human migration into the Pacific''.
She was also "a great communicator'' who had engaged and motivated the public about her science, Prof Hayne said.
Prof Matisoo-Smith's research mainly focuses on using genetic evidence to track human migration and settlement of the Pacific using leading-edge molecular biology techniques.
