This study aimed to use a computer-controlled touchscreen system to examine visual discrimination in Garrano horses (Equus caballus), an endangered breed of pony belonging to the Iberian horse family. This pilot study focused on the perceptual similarity among letters of the alphabet. We tested five horses in a one-male unit (OMU) living permanently in a semi-free enclosure near their natural habitat in Serra d’Arga, northern Portugal. Horses were trained to nose-touch black circles that appeared on the screen. Then, they were tested for discrimination of five letters of the Latin alphabet in Arial font, namely O, B, V, Z, and X, using a two-choice discrimination task. The confusion matrix of letter pairs was used to show the MDS and to identify the relative contribution of shape features. The results showed perceptual similarities among letters with curvatures pitted against those of straight lines. Shape perception in horses seems to share features with that of humans and other animals living in different niches. The touchscreen system proved to be an objective and innovative way of studying cognition in the socially organized group of horses. The automated system can promote the welfare of captive horses by maximizing their freedom of movement.