Genetic anthropology is the branch of anthropology where research has been very active in Tunisia since the 1980is. At least three generations of Tunisian geneticists have generated large amounts of data about the genetic makeup of the Tunisian population, bringing valuable insights into the historical migration and admixture events, during the last 3000 years. These results have, however, stimulated several controversies about the Berber and the Arab genetics components, which strongly arouse after the 2011 revolution, nourished by political division about the “identity” of Tunisians. Some political fractions (Islamists) strongly claimed the Arab origin of current Tunisians while others defended their specificity both genetically and socio-cultural level. The first studies published between 1984 and 2000 have used markers systems such as ABO blood groups or Immunoglobulin allotypes and some genes of medical relevance, to address the genetic diversity of the Tunisian population and some of its ethnic minorities. These were followed (between 2001-2016) by studies using DNA markers such as Alu-sequences, autosomal or Y-chromosome microsatellite markers or mitochondrial DNA markers. More recently, genome wide markers (SNPs, whole exome, and whole genome sequences) have been used in comparative studies of populations from North Africa (including Tunisia), Sub-Saharan Africa and southern Europe, mainly led by European scientists. These studies have supported different pictures of the Tunisian population, with somehow conflicting results, where some studies advocated a highly admixed population with the presence of both Berber and Arabic genetic components, while others underlined the specificity of Tunisians compared to other North Africans. The new data on whole genomes of 150 Tunisians sampled in all country regions might end the controversy.