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The present study was undertaken to genetically evaluate Caspian horses for genetic diversity and to asses whether they have experienced recent population bottlenecks. A total of 100 individuals were characterized for within breed diversity using 16 microsatellite markers. The estimated mean number of alleles was 8.69 per locus, with a total of 139 alleles in the genotyped sample. The mean effective number of alleles in the Caspian horse population was 5.86, ranging from 3.49 to 8.49. The average observed heterozygosity in the present study (0.52) was lower than to the expected heterozygosity (0.82), which may reflect the narrow genetic base of the current population of this breed. All marker loci employed in this study were very informative with an average of 0.80. The Chi-square and likelihood ratio tests performed to examine population for HWE showed some highly significant deviations from HWE. Estimated values of Wright’s fixation index, FIS (0.367) indicates a certain level of heterozygote deficiency. A significant heterozygote excess on the basis of different models, as revealed from Sign and Wilcoxon rank test suggested that Caspian horse population is not in mutation-drift equilibrium. But, the Mode-shift indicator test showed a normal ‘L’ shaped distribution for allelic class and proportion of alleles, thus indicating the absence of bottleneck events in the recent history of this breed. The present work is a contribution to the knowledge of population structure and to the assessment of genetic diversity that may be helpful to horse breeders in designing and managing breeding or conservation strategies for the Caspian horse breed.

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