Equoid perissodactyls were diverse in the Eocene of the Iberian Peninsula, and those from the central and western Iberian basins (Mondego, Oviedo, Almazán, Duero, and Miranda-Treviño) and the eastern Ebro Basin (Ulldemolins area) were endemic, with the presence of six genera and 19 species (mainly Palaeotheriidae sensu stricto) that are unknown in the rest of western Europe. In this paper, a new endemic Eocene paleotheriid genus, Idiodontherium, gen. nov., is reported. The new genus includes two species: I. martindejesusi, from the upper middle Eocene (Bartonian) of Mazaterón (Almazán Basin, Soria, Spain) and I. astibiai, from the upper Eocene (Priabonian) site of Zambrana (Miranda-Treviño Basin, Álava/Araba, Spain). Idiodontherium exhibits an unusual dental pattern, which is characterized by an extreme shortening of the jugal series due to a great reduction of the premolar series, in combination with a long post-canine diastema. It is a small to medium-sized plagiolophine with thick enamel in comparison with other plagiolophine equoids of the same size. These new taxa exhibit peculiar dental features that could be associated with greater specialization of the diet.