Abstract In the present study, genetic analyses of diversity and differentiation were performed on five Algerian horse breeds (Barb, Arab-Barb, Arabian, Thoroughbred and French Trotter). These breeds of horses are distinct not only because of their adaptation to different agroclimatic conditions prevailing in the country, but also because they have unique performance traits. In this research a total of 200 animals were genotyped for 11 microsatellite markers. We registered the individuals chosen in the breed�s studbook and we avoided closely related animals. All five populations (Arab-Barb, Arabian, Barb, Thoroughbred, and French Trotter) had high heterozygosity values (0.75, 0.71, 0.72, 0.71, and 0.69 respectively). These values are among the highest heterozygosity values reported for other horse populations using the same microsatellite markers. A genetic diversity analysis was conducted both within and between the five horse breeds. Three different approaches: genetic distances, factorial correspondence analysis and discriminant analysis of principal components were considered to study genetic relationships among these horse populations. The native Algerian breeds were clearly differentiated from the others. Small genetic distances and high admixture level recorded between Barb and Arab-Barb breeds are probably due to a large gene flow among them. The data and information found in this study can be utilized in the organization of conservation programs planned to reduce inbreeding and to minimize loss of genetic variability. Key words: Algeria, genetic analyses, Microsatellite markers, horse breeds, conservation programs.

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