Even animal names can become contentious in politics
The environment ministry says the Latin names of the red fox, the wild sheep and the roe deer will be altered.
The red fox for instance, known as Vulpes Vulpes Kurdistanica, will now be known as Vulpes Vulpes.
Turkey has uneasy relations with neighbouring Armenia and opposes Kurdish separatists in Turkey.
The ministry said the old names were contrary to Turkish unity.
“Unfortunately there are many other species in Turkey which were named this way with ill intentions. This ill intent is so obvious that even species only found in our country were given names against Turkey’s unity,” a ministry statement quoted by Reuters news agency said.
Some Turkish officials say the names are being used to argue that Armenians or Kurds had lived in the areas where the animals were found.
Turkey has tense ties with its eastern neighbour Armenia, which it does not officially recognise.
Armenians accuse Turkey of genocide, saying 1.5 million of their people died or were deported from their homelands under Turkish Ottoman rule.
Turkey denies the genocide and says the death count is inflated.
For the last two decades, Turkey has also been fighting Kurdish separatists, who have sought an independent state in Turkey’s south-east.