The origin of the Appenzeller Sennenhund have been a subject of discussion, and there are two main theories; the first is that the Appenzeller has its beginning with the Roman dogs brought over the Alps, the second theory is that the breed has the ancient Swiss spitz as its ancestor.
The Appenzeller is related to the other breeds of Swiss Mountain Dogs, there is no doubt about that, and should therefore, according to history, contain blood from the Roman dogs. But the tail gives the breed away, and it is pretty sure that also the Swiss spitz have played an important role in the origin of the Appenzeller. Which means that the Appenzeller Sennenhund has both Molosser dogs and spitz in its extended pedigree.

It is believed that the Appenzeller has a long history in the Appenzell region where inbreeding has formed the modern breed. The Appenzellers work, first and foremost, have been a cattle drover, to control the cattle at the farm and at the pastures, but also to bring the cattle to the market. The breed was also used as a herd guardian, as a draft animal and as a farm watchdog.
It was in the book "Tierleben der Alpenwelt" (Animal Life in the Alps), published in 1853, that the breed was described for the first time; "a clearly barking, short haired, medium size, multicolour cattledog of a quite even "Spitz type", which can be found in certain regions and is used partly to guard the homestead, partly to herd cattle".
Max Siber was the first man that brought attention to the Appenzeller, when he in 1895 encouraged the Swiss Kennel Club to pay attention to the breed. A comitee was set up, given a mandate to form a standard, and set out for a search for suitable breeding dogs. In 1898 they found 9 males and 7 females of good breeding quality. However, in 1899 Mr. Siber died, and the Appenzeller lost their greatest spokesman. Once more, Prof. A. Heim came to the rescue of the Swiss dog breeds, and without Mr. Heim's efforts the Appenzeller surely would have gone extinct.
In 1906 Mr. Heim and 10 of his friends formed a club for the Appenzeller, which soon arranged shows for the breed, wrote a stud book, and guided the early breeders. In 1914 Mr. Heim wrote the first standard of the breed.

The first members of the breed was included in the stud book with "unknown" origin. The Appenzeller breeding of today is almost entirely based on the first eleven dogs that was registred, which means that there is a high degree of inbreeding in the dogs of today. Despite of the low number in the foundation stock there were not practized any line-breeding, since the owners, mostly farmers, did not pay any attention to beauty, but wanted a watchful and workable dog.
The breeders formed two camps; the ones that wanted a light Appenzeller, and the ones that wanted a large a more powerful dog. The light variant was 48-50 cm. (18,8-19,6 in) at the withers, while the larger variant was 55-60 cm (21,6-23,6 in). (Today the height of the Appenzeller Sennenhund is between 50 and 58 cm. (19,6-22,7 in).
Heim sain in 1919 that the built of the Appenzeller should be regarded as of greater importance than the colour. Even so, the yellow and brindle Appenzeller's have dissapeared, as well as the ones with a white ring around the neck and the ones with a white sock. Still today dogs with the white ring around the neck or with a white sock or two are born, but they are culled or left out of the breeding.

Approximately 500 to 600 pure bred Appenzeller's is listed in the stud book, and even if the breed is still "thin on the ground" outside of Switzerland, it slowly gains in numbers in other countries than its native.