Investigation of genetic relationship among populations was traditionally based on the analysis of allele frequencies at different loci. The aim of this study was to analyze, the genetic diversity and variability of three native Iranian goat populations (Raeini, Korki Jonub Khorasan and Lori) through the use of 13 microsatellite markers. The 13 tested loci were all polymorphic in the three goat populations. Within the 13 polymorphic loci, allele frequencies, number of effective alleles (Ne), heterozygosity (He), polymorphism information content (PIC) and Nei's standard genetic distance (D) were calculated, and UPGMA phylogenetic tree was constructed based on allele frequencies. The average number of alleles was 7.57, ranging from 3 to 13 at the 13 assessed loci. The average values of Ne, He and PIC of all loci were 5.14, 0.797 and 0.757, respectively. Korki Jonub Khorasan showed the highest mean number of alleles (8.15), while the highest value for polymorphic information content was observed for Raeini population (0.78). Tests of genotype frequencies for deviation from the Hardy-Weinberg equilibrium (HWE), had been tested in the level of probability (p<0.005). A UPGMA diagram based on Nei's standard genetic distances, yielded relationships between populations that agreed with what is known about their origin, history and geographical distribution.

Key words: Hardy-Weinberg equilibrium (HWE), goat, diversity, microsatellite.