The breeding history of the Einsiedler horse is closely connected with the Benedictine cloister Einsiedeln. In the mid‐nineteenth century, it was decided to use European Warmblood stallions for cross‐breeding and to abandon the selection of stallions. Since that time, it has only been possible to trace back the origin of Einsiedler horses using maternal ancestry information. Here, we collected high‐density genotype data for European Warmblood horses (Selle Français, Swiss Warmblood and Einsiedler) and Franches‐Montagnes horses, the last native Swiss horse breed, to unravel the current population structure of the Einsiedler horse. Using commonly applied methods to ascertain fine‐scale population structures, it was not possible to clearly differentiate the Einsiedler from other European Warmblood horses. However, by means of runs of homozygosity (ROH) we were able to detect breed‐specific ROH islands for the Einsiedler horse, including genes involved in domestication and adaptation to high altitude. Therefore, future breeding activities should involve the screening of these breed‐specific ROH segments, the revival of cryopreserved sperm and the selection of Einsiedler stallions.