¹Animal Science Research Institute of Iran (ASRI), Agricultural Research, Education and Extension Organization (AREEO), Karaj, IRAN DOI : 10.9775/kvfd.2016.17096 Microsatellites are a class of genetic markers commonly used for parentage verification and population studies. This study determined the efficiency of microsatellite markers for identification and pedigree analysis in horses based on the example of Turkmen horse population. For this purpose, 748 Turkmen horse samples including 574 adults (92 stallions, 345 males and 137 mares) and 174 foals (98 colts and 76 fillies),were genotyped by using seventeen microsatellite markers recommended by ISAG. The number of allele per locus varied from 5 (HMS01 and HTG07) to 10 (HTG10) with an average value of 7.65. The observed heterozygosity and the expected heterozygosity ranged 0.365-0.953 (mean 0.703), from 0.617-0.884 (mean 0.792) respectively. PIC value ranged from 0.586 (HTG7) to 0.873 (HTG10) with average 0.767. The total exclusion probability of the 17 microsatellite loci was 0.9999. The pedigree study of the Turkmen horse using microsatellite markers was efficient in detecting mistakes during genealogical records. These results suggested that the DNA typing method had high potential for systematic control of the genealogical registrations and genetic resources to improve genetic aspects in Turkmen horses. Keywords : Parentage verification, Genetic characterization, Microsatellite markers, Turkmen horse