Natural Trap Cave is an enigmatic site in Wyoming that has been accumulating fossils for tens of thousands of years from animals falling into it. One of the more common taxa present at this site are horses. North American equids have been separated into two main groups: caballine “stout legged” horses, which include the modern Equus ferus caballus; and the extinct non-caballine so-called “New World Stilt Legged” horses, which possess more gracile distal limb elements than modern horses. Genetic evidence has shown that both taxa are present at the Natural Trap Cave site. While post-cranial elements of both have been found, the most common horse specimens recovered have been isolated teeth, which have historically been difficult to identify to a specific taxon, though recent studies have been successful using geometric morphometrics on the occlusal surfaces of cheek teeth to differentiate equid taxa and populations. This study also uses geometric morphometrics to attempt to differentiate upper cheek tooth specimens between caballine and non-caballine stilt legged horses from Natural Trap Cave. Two landmark schemes were employed, one with fewer landmarks, and one with greater coverage, including sliding semi-landmarks. These schemes were used first on a dataset of only known specimens that had been taxonomically identified, and then unknown specimens from Natural Trap Cave were added. These analyses showed that the two taxa do indeed occupy statistically significant different areas of morphospace, as do premolars and molars. Surprisingly, the smaller landmark scheme produced better resolution on the Principal Components Analysis plots, possibly because the larger landmark scheme introduced ontogenetic variation due to different levels of tooth wear. While definitive identification does not seem advisable with this methodology, the unknown specimens grouped more with the known stilt legged specimens, suggesting that this taxon was more prevalent at Natural Trap Cave than the caballine Equus.