The collection would fetch €29 million ($42.32 million) on the black market, the Civil Guard said Sunday in a statement, adding that its owner could be charged with trafficking and other crimes against the environment.
It said the finding was the largest of protected stuffed specimens in Spain.
Investigating agents found the stuffed animals in two warehouses extending over 50,000 square metres on the outskirts of Bétera, a small town north of the eastern coastal city of Valencia.
Of the 1090 stuffed animals found, 405 belonged to specimens protected by the CITES convention on wildlife protection.
They included the scimitar oryx, also known as the Sahara oryx, which the International Union for the Conservation of Nature, or IUCN, declared extinct in the wild in 2000, and at least two more species nearly extinct: the addax, or white antelope, originally from the Sahara desert and the Bengal tiger.
The agents also recorded stuffed specimens of cheetah, leopard, lion, lynx, polar bear, snow panther and white rhinoceros, among others, as well as 198 large ivory tusks from elephants.
The Civil Guard said it would investigate whether any documents exist justifying the ownership of the collection.