They were imported from Sweden to Estonia in large numbers, thus lived mixed with Estonian native horses and the genetic backgrounds prove that there are lot similarities between them.During the 11th century a well known explorer Adam of Bremen said that the Estonians are rich with gold and good horses. Later on, during the 14th and 15th centuries, the Estonian native was mainly exported to Sweden for war purposes and many were sold to Russia for farm work.The breed was documented for the first time in 1856, when breeders attempt to improve the breed. At that period the breed was crossed with other light working and riding horse breeds. The best result of the crossbreeding with the Hackney was the foundation of the Tori horse. Vansikasa was a well known Estonian sire with exceptional strength that was foaled on the Tori stud. One of his daughters was the founding mare of Tori horse breed. There are several Baltic horse breeds influenced by the Estonian, including the Russian Vyatka horse. The crossbred with the Ardennes resulted with a creation of the Estonian Draft. A recent crossbreeding with the Finnhorses resulted with an improvement of their size and in 2005, 25 Estonian Natives were imported to Sweden to recreate the land horse, which is now known as the Estonian Bush Pony.
Since the end World War I, a breeding program began in order to preserve the breed and make up for the big losses from the war. The first studbook was opened in 1921, in the same year when was established the Estonian Native Horse Breeders Society. In 1937 there were only 13 stallions and as the mechanization and the agriculture grew, the breed was almost extinct, except in the islands of Saaremaa and Hiiumaa. A new breeding program was created and saved the breed from extinction reaching a number of 1000 Estonian Native horses, which are most common in Estonia.