The Stewart shag is actually two species, scientists have discovered.

A University of Otago-led team of international researchers have published findings in the latest edition of the Zoological Journal of the Linnean Society. In their research, they describe how they used DNA and morphometric analysis to compare ancient and modern populations of shags around Stewart Island and parts of the South Island, discovering that the Stewart shag is in fact two separate species.

The two species are the Foveaux shag (living along the Foveaux Strait and Stewart Island) and the Otago shag (living around the Otago Peninsula).

University of Otago postdoctoral research fellow Dr Nic Rawlence said the findings were surprising.

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"We found a very distinctive pattern, where shag populations from Otago (Otago shag) differed from those around Foveaux Strait/Stewart Island (Foveaux shag) in terms of DNA, body size, breeding time and the proportion of pied (black and white) and dark bronze plumage variations within the population," he said.

"Scientists have suspected that these two formerly unrecognised species were different as far back as the mid-late 19th century, but we have not had the genetic or analytical tools to address this question until now."

University of Otago professor Hamish Spencer, who was also involved in the study, called the discovery exciting.

"New Zealand is home to more shag and cormorant species than anywhere else in the world. This discovery emphasises yet again how special our bird fauna is on a worldwide basis."

Project leader Dr Martyn Kennedy - also from the University of Otago - said implications from the research included looking at ways to ensure the survival of both shag species.

"The Otago and Foveaux shags will require subtly different conservation strategies," he said.

University of Otago professor Jon Waters, who was also involved in the study said the new recognition of endemic wildlife - species unique to our region - should add value to our ecotourism industry.

Researchers from the University of Otago led the project, with support from the Canterbury Museum, Museum of New Zealand Te Papa Tongarewa, Otago Museum, the Natural History Museum (London), and the Muséum National d'Historie Naturelle in Paris.

Funding came from the Marsden Fund and Allan Wilson Centre.