Iran is one of the most important mohair-producing countries in the world. Markhoz goat is the only breed producing mohair in Iran that is showing endangerment trend in its native breeding region. The aim of this study was to evaluate the genetic diversity of Markhoz goat and its color types using ISSR markers. Four primers were designed and two of them were selected based on their number of bands and polymorphic properties. These primers generated a total of 28 amplification products, from which 23 bands were polymorphic, revealing 82.14% polymorphism. The average ( ± standard error) of gene diversity (h) in Markhoz goat was 0.34 ± 0.18. The study of genetic diversity in Markhoz color types (Saddle Brown, Sandy Brown and Black) determined that total heterozygosity (Ht), heterozygosity within color types (HS) and the diversity between color types (Dst) were 0.33, 0.30 and 0.03, respectively. The coefficient of population differentiation (Gst) was 0.91. These results indicate that the genetic variation between color types is a small part of the total heterozygosity. The genetic distance between colors types using Nei standard genetic distance and Nei unbiased genetic distance methods was calculated. Phylogenetic danderogram of color types grouped Saddle Brown and Sandy Brown types in one cluster and Black types in another cluster that in agreement with their phenotypic similarities. The results obtained from genetic diversity of color types indicated that the highest and lowest genetic diversity exist in Saddle Brown and Black color types, respectively. Then it seems, to conserve all color types, the breeding programs should be conducted to improve genetic diversity in Black color type
