The Iberian Peninsula, rich in archaeological and anthropological records, has experienced significant population migrations throughout history, including Celts, Romans, and Muslims. The city of Mérida, an important city during the Islamic period, experienced important transformations, especially after the fall of the Umayyad caliphate. In 2009, an archaeological excavation uncovered a large Islamic cemetery (maqbara), dating from the 8th to 12th centuries. From this maqbara was selected 70 individuals from the site “Former Military Artillery Barracks Hernán Cortés”, and 14 from the site “14 Jose de Larra Street”. Dental nonmetric traits are reliable indicators of gene flow and genetic affinity among populations. To evaluate the biological affinities of these 84 individuals we recorded 22 dental traits using the ASUDAS system and compared with them to ten reference samples. The biodistances were tested with the Mean Measure of Divergence statistic. Biodistance analysis results showed close biological proximity between the Merida sample and South European references samples, with intra-regional heterogeneity among Iberian Peninsula populations. The strategic location of the Iberian Peninsula between North Africa and Southern Europe facilitated genetic and cultural interactions, shaping its genetic landscape. This study emphasizes the complex relationship between historical, demographic, and cultural factors influencing the genetic variability of the Merida sample.