The Spanish Merino is the most significant sheep breed globally due to its economic and cultural importance in human history. It has also had a substantial influence on the development of other Merino and Merino-derived breeds. Historical sources indicate that crossbreeding to produce finer, higher-quality wool was already taking place in the south of the Iberian Peninsula during the Roman era. This evidence suggests that individuals with a racial pattern very similar to that of the modern Merino may have already existed on the peninsula. The presence of skeletal remains of these animals at various human settlements dated to the late fourth and third millennia BC could provide insights into the genomics of these ancestral sheep. This study analyzes ancient DNA extracted from nine skeletal remains from three archaeological sites in southern Iberia, dated to the third millennium BC. The samples were sequenced and aligned with the ovine genome. The genetic distances observed among the samples indicate a closer relationship between several animals from the Marinaleda (Seville) and Grañena Baja (Jaén) sites, suggesting possible shared livestock practices among these communities, while this was not evident at the La Minilla site (La Rambla, Córdoba). The varying ages of sacrifice or death identified in the faunal studies of the sites producing the samples suggest a focus on meat exploitation at La Minilla (La Rambla, Córdoba), while in Grañena Baja (Jaén) and Marinaleda (Sevilla), the emphasis appears to have been on the use of secondary products. The genomic results of the nine Ovis aries individuals support this hypothesis.