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See also: Genetic history of the Iberian Peninsula

Spain's Morisco population was the last population who self-identified and traced its roots to the various waves of Muslim conquerors from North Africa. Historians generally agree that, at the height of Muslim rule, Muladis or Muslims of pre-Islamic Iberian origin were likely to constitute the large majority of Muslims in Spain. However, it is difficult to make such an assertion about the Morisco minority by the 15th and 16th century. Modern population genetics generally assume Moriscos to have had both significant Iberian and North African ancestry, even if, after centuries of presence and intermarriage in the Iberian peninsula they were unlikely to differ significantly in ethnic terms from the wider Spanish population. For this reason, studies in population genetics which aim to ascertain Morisco ancestry in modern populations search for Iberian or European genetic markers among contemporary Morisco descendants in North Africa, and for North African genetic markers among modern day Spaniards.

A wide number of recent studies of modern day Spanish and Portuguese populations have ascertained an unusually high level of North African admixture, which is generally attributed to Islamic rule and settlement of the Iberian peninsula. Common North African genetic markers which are relatively high frequencies in the Iberian peninsula and are largely absent in the European continent are Y-chromosome E1b1b1b1(E-M81) and MtDna Haplogroups L and U6. Studies coincide that North African admixture tends to increase in the South and West of the peninsula, peaking in parts of Andalusia, Extremadura and North West Castile. Distribution of North African markers and largely absent from the North East of Spain as well as the Basque country. The uneven distribution of admixture in Spain has been explained by the extent and intensity of Islamic colonization in a particular area, but also by the varying levels of success in attempting to expel the Moriscos in different regions of Spain , as well as forced and voluntary morisco population movements during the 16th and 17th centuries.

As for tracing Morisco descendants in North Africa, to date there have been few genetic studies of populations of Morisco origin in the Maghreb origin although studies of Moroccan population have not detected significant recent genetic inflow from the Iberian peninsula. A recent study of various Tunisian ethnic group have found that all were of indigenous North African group, including those who identified as Andalusians.

Spain's Morisco population was the last population who self-identified and traced its roots to the various waves of Muslim conquerors from North Africa, despite the fact that after eight centuries of Muslim rule in Spain, they did not differ significantly in ethnic terms from the wider Spanish population. A number of studies have tried to find out the genetic impact of North African and Middle Eastern population movements on the modern Spanish and Portuguese ancestry, through comparison of genetic markers in Spain and Portugal with North Africa and the Near East. The most recent and thorough study of Moorish influence in the Iberian Peninsula was conducted in April 2013 by Pompeu Fabra University using genome-wide SNP data for over 2000 individuals. This study concluded that the Iberian Peninsula holds higher levels of both North African and Sub-Saharan ancestry than the rest of the European continent. Estimates of shared ancestry with North African populations were found to be higher than previously reported, accounting for between 4% and 20% of individual genomes in southwestern European populations, whereas these do not exceed 2% in southeastern European populations outside Spain and Portugal.

Priorly, Capelli et al. 2009 reported that North African male haplogroups, especially E1b1b1b (E-M81), E1b1b1a-b (M78 derived chromosomes showing DYS439 allele 10, or E-V65) and a subset of J1 (M267 derived), represented, on average, 7-8% of the current Iberian male lineages.

A number of studies focus on the genetic impact of the Morisco community on the modern Spanish population. Iberia has a presence of the typically North African Y-chromosome haplotype marker E-M81, that is not absent in the rest of Europe. and Haplotype Va. A thorough Y-chromosome analysis of the Iberian peninsula reveals that haplotype E-M81 surpasses frequencies of 10% in Southern Iberia. As for Mtdna analysis (Mitochondrial DNA), although present at only low levels, Iberia has much higher frequencies of typically North African Haplogroup U6 than those generally observed in Europe. It is difficult to ascertain whether U6's presence is the consequence of Islam's expansion into Europe during the Middle Ages, or it is rather the result of ancient demic processes that predate the Islamic presence.

According to a widely publicized recent study (December 2008) published in the American Journal of Human Genetics, 19.8 percent of modern Iberians (Spain + Portugal) have DNA reflecting Near Eastern and 10.6 percent having DNA reflecting North African ancestors.

According to another DNA study by the University of Leeds (2008) of the Y chromosome amongst the current population of Iberia suggests that 11% of Iberian males have traces of Moorish ancestry.