"But when we started doing DNA work, we found out they were genetically very different - they had different demographic histories, and different skull and bone shapes."
The birds also varied in plumage and breeding times: but the mystery was only able to be fully solved using new genetic and analytical tools.
In another twist, ancient DNA and morphometric analysises, comparing ancient and modern populations of shags, showed the two may not even be sister species.
Several tests of the Otago shag's lineage found it was more closely related to the endemic Chatham Island shag.
Study co-author Professor Hamish Spencer said New Zealand was home to more cormorant species than anywhere else in the world.
"This discovery emphasises yet again how special our bird fauna is on a worldwide basis."
The finding further raised the need for a slightly altered conservation strategies for the newly-described shags.
"While the Foveaux shag has been little affected by humans, Otago shag populations along the east coast of the South Island were devastated, possibly losing more than 99 per cent of their population size within 100 years of human arrival," said study project leader Dr Martyn Kennedy.
These once heavily-hunted mainland populations now occupied just a fraction of their prehistoric range, having never really recovered, he said.
"There is now the real possibility of reintroducing the Otago shag to formerly occupied areas along the eastern South Island."
The study, published this week in the Zoological Journal of the Linnean Society and supported by the Marden Fund and now-closed Allan Wilson Centre, followed recent findings lifting the lid on a previously-unknown population of little blue penguins from Australia.
After identifying the Otago population of penguins as distinct from our endemic species and hailing from across the Tasman, researchers this month confirmed they arrived on our shores as recently as the past few hundred years.
Professor Jon Waters, who worked on both the penguin and shag studies, said this week's findings again highlighted that there is still much to be discovered about New Zealand's unique biota.
"The new recognition of endemic wildlife - species unique to our region - should add value to our ecotourism industry."
The researchers now have more New Zealand species in their sights for new DNA-based investigations.
The new study included team members from the University of Otago, as well as Canterbury Museum, Museum of New Zealand Te Papa Tongarewa and Otago Museum, along with the London-based Natural History Museum and the Paris-based Museum National d'Historie Naturelle.
