The Apulian Peninsula represents a key-region for the study of climatic changes and paleoenvironmental dynamics during the Quaternary. Both large and small-sized horses are well documented in this region during the Pleistocene and are frequently found associated. The caballoid horses from Middle to Late Pleistocene of Europe show a large intraspecific ecomorphological variation, emphasizing a strong link between skeletal adaptations and specific aspects of the palaeoenvironment. This large variability led to an extended debate concerning the taxonomy of equids and their evolutionary history. In the Italian Peninsula, fossils from the Middle to the Late Pleistocene have been historically referred to several species (or even subspecies), emphasizing the uncertainty of the taxonomic attribution. Here, a large craniodental sample of Equidae fossils from late Middle Pleistocene to the Early Holocene localities of the Apulia Peninsula are described for the first time. The comparison of the protocone index allowed us to determine the first occurrences of Equus mosbachensis von Reichenau, 1903 in the Apulian Peninsula, from a few localities chronologically referred to late Middle Pleistocene. Most of the material from the late Middle to the end of the Late Pleistocene is instead attributed to Equus ferus Boddaert, 1785. The results of this work thus add novel information on the biochronology of Italian fossil equids and their evolutionary history through the Middle and Late Pleistocene.