Northwestern Africa has long served as a geographic and cultural link between Africa, Europe and the Near East, yet its ancient population history remains underrepresented in genomic research. This is partly due to poor DNA preservation in warm and humid climates, which limits the recovery of authentic ancient DNA (aDNA). In this thesis, ancient genomic data from human remains excavated from 12 archaeological sites in present-day Morocco were analysed to investigate population structure, genetic continuity, and admixture across approximately 2500-626 years before present. The dataset spans several major historical periods, including the Iron Age, Phoenician/Punic expansion, Roman influence and the Arab-Islamic expansion. Population genetic analysis showed that the individuals cluster within a broad North African-Mediterranean genetic space, with affinities to ancient North African, Iberian and Levantine-related reference groups. Principal component analysis, ADMIXTURE and f statistics suggest that between approximately 2500 and 626 years ago, the ancient Northwestern African gene pool was composed of several Mediterranean genetic ancestries, with significantly higher Iberian-associated affinities than broadly contemporary populations from present-day Tunisia, located further east. Several examples of within-site genetic heterogeneity reflect admixture of different genetic ancestries. This supports the interpretation of ancient Morocco as a dynamic region shaped by Mediterranean and trans-Saharan connectivity, rather than genetic isolation.