Genetic diversity of 38 almond local genotypes was investigated using RADP and ISSR markers with the analysis of nut morphology.Samples were taken from five locations for this study, including Sharbazher, Mergapan, Qaradakh, Barznja, and Hawraman.Almond nuts width, length and thickness were studied and their mean values were observed to range between 16.18-27.21mm, 24.18-41.07mm and 11.49-16.81mm, respectively.Polymorphic bands of mean values were 9.5 for random amplified polymorphic DNA (RAPD) and 8 for inter-simple sequence repeat (ISSR).The PIC values were recorded for RAPD primes to range between 0.77 to 0.97 and those for ISSR primers were also verified between 0.36 to 0.97.Based on Jaccard similarity coefficients, the genetic distances were recorded between 0.32 (B-G3 vs. B-G4) (M-G2 vs. M-G1) to 0.75 (H-G5 vs. Q-G1) and all genotypes were grouped into 3 major clusters (A, B and C) with a mean dissimilarity 0.535 for 20 RADP markers.In the case of the 15 ISSR markers, a genetic distance between 0.19 (H-G13 vs. H-G12) to 0.78 (H-G5 vs. B-G6) was also observed, with four clades (A, B, C and D) with a mean dissimilarity of 0.485.According to STRUCTURE analysis, all genotypes were divided into two groups.Analysis of molecular variance (AMOVA) demonstrated a high-level genetic differentiation within a population 88% for RAPD and 87% for ISSR.
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