Background Throughout the past few years, a lively debate emerged about the timing and magnitude of the human migrations between the Iberian Peninsula and the Maghreb. Several pieces of evidence have pointed to a complex and intermingled evolutionary history in the western Mediterranean area. Methods Biological samples from both southern Iberia and Morocco have been previously used in other genetic diversity studies based on uniparental and autosomal markers. A total of 142 western Mediterranean individuals were genotyped at the Spanish National Cancer Research Center in the Human Genotyping laboratory. Key findings Results allowed the researchers to trace a detailed view of the genomic composition of the western Mediterranean human metapopulation at the crossroads between Europe and Africa. Local ancestry inference analysis showed a significant differential contribution of the sub-Saharan African ancestral panel among southern Iberian subpopulations. Conclusion Migration time modeling showed recent historic dates for the admixture events occurring both in Iberia and in the North of Africa. However, an integrative vision of both paleogenomic and modern DNA data allowed the researchers to detect chronological transitions and population turnovers. This could be the result of transcontinental migrations dating back from Neolithic times. The present contribution aimed to fill the gaps in the modern human genomic record of a key geographic area, where the Mediterranean and the Atlantic come together.