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Analysis of molecular genetic diversity of dromedaries (Camelus dromedarius) in Tunisia. The objective of this study was to investigate the genetic diversity and relationships among Tunisian camel populations in three different geographical locations (Kebili, Medenine and Tataouine) from Southern arid and semi-arid regions in Tunisia. Eight selected microsatellite markers were used for a sample of 90 dromedary genotypes. A total of 34 alleles were detected in the three populations. The number of alleles per locus varied from two to seven with an average of 4.25 alleles per locus. For each population the average of alleles per locus is 3.33, 3.71 and 3.87 for Kebili, Medenine and Tataouine, respectively. The mean of the observed heterozygosity (H(o)) were 0.43, 0.50, 0.57 and 0.52 for Kebili, Medenine, Tataouine and total populations, respectively. These values were lower than expected with heterozygosity (H(e)) values 0.50, 0.57, 0.62 and 0.61, respectively. The average inbreeding coefficient was 15.3% in Kebili, 11.4% in Medenine and 8.3% in Tataouine. The mean estimates of F-statistics were F(IT) = 0.15, F(IS) = 0.071 and F(ST) = 0.083. These values were significantly different from zero (p < 0.05) and suggest a moderate differentiation. An inbreeding rate of 15% was found. Estimated genetic distances revealed by the loci varied from 0 to 0.9 between dromedary individuals. The estimated genetic distances pair-wise showed 0.104 among Medenine-Tataouine, 0.280 between Kebili-Medenine and 0.290 between Kebili-Tataouine. The distance matrix was able to distinguish between two separate genetic entities: Nefzawa (Kebili) including Merzougui, G’oudi and M’hari ecotypes and the Aaradh group (Medenine and Tataouine) that includes Maghribi and Khaouar ecotypes. The results of this study did not confirm the present classification established by dromedary herders who divide the population into five different ecotypes, apparently based on the sociogeographical criteria. These preliminary results showed that microsatellites are promising tools for breed characterization. They indicated that the populations under investigation have a high genetic variability and would be suitable as genetic stocks for conservation and sustainable utilization programs.