I can expand on this and answer specifically the question in the title. Organisms are classified based on how closely related they are to one another, not based on a single morphological trait, but a morphological trait can be a convenient way to distinguish between two groups. Even when phylogenies are built from morphological data (not common in the age of molecular biology) they use dozens of traits, which can be as simple as number of toes, but more often are measurements of different body parts or ratios of those measurements. It might be just as correct to say that Perissodactyla and Artiodactyla are distinguishable by the ratio of femur length to pelvis width (just for example, not a real measurement they used), but number of toes is much more convenient.