Abstract: The objectives of this study were to assess the genetic variability among six Iranian goat breeds including: Markhoz (MR), Korki of South Khorasan (KK), Black Lori (BL), Najdi (NJ), Korki of Raeini (KR), Tali (TL) and to evaluate the genetic relationships between populations using RAPD markers. The genetic characterization of these genetic resources is essential to conservation and breeding programs. Blood sample (50 individuals per breeds) were collected from spreading location of these breeds. DNA extraction was carried out by Salting-Out method. Initially, a total of 16 ten and eleven-nucleotide arbitrary primers were used but 10 of 16 primers revealed a pattern with scorable amplified bands. From a total number of 115 scored bands 62 (53.9%) and 53 (46.1%) were described as polymorphic and monomorphic, respectively. The average number of bands per primer 11/5 and with sizes varying from 220 to 2310 bp in length. Nei’s genetic distances varied between 0.081 and 0.227 in the populations. The phylogenetic tree was reconstructed on Neighbor-Joining method and showed two main separated groups. One includes KK, TL, KR in a branch and then NJ. Another consists BL and MR. This research was showed that RAPD technique is an useful tool for evaluation of genetic variation among of domesticated animals.