Halabja governorate in the Kurdistan region-Iraq is famous for having high-quality pomegranate accessions. The current study was conducted to evaluate the morpho-phytochemical amount of pomegranate functional food and the genetic diversity as an important tool for the characterization of the genetic resources for germplasm management and the identi cation of the best genotypes for genetic improvement. In this study, phenotypical parameter, highly signi cant morphometric differences (P ≤ 0.05) among 24 genotypes, with the mean values of fruit weight, peel thickness, and weight of 100 Arils, total avonoid content (TFC) and total phenolic content (TPC), antioxidant activity, total soluble solid content (TSS) 299.21 g, 3.47 mm and 38.59 g, 54.50,47.97 µg/ml, 21.08 µg/ml and 14.59 Brix respectively. In addition, inter-simple sequence repeat (ISSR) was utilized to assess the genetic diversity of the collected pomegranate genotypes. Twelve random primers of produced products plus a number of the ampli ed primer bands ranging from 3 to 12 and total number of 83 ampli ed bands were produced, among which 78 bands were polymorphic and 5 bands were monomorphic. The highest, lowest, and mean values of polymorphic bands were (11, 3, and 6.5), respectively. The PIC values ranged from 0.58 to 0.90. The dendrogram clusters for all the selections showed dissimilarity coe cients ranging between 0.22 to 0.23 (G4 vs. G5) to 0.63 (G13 vs. G14), and ve groups (A, B, C, D, and F) with a mean dissimilarity (0.49). According to the results, morphometric and biochemical properties are signi cant aspects of development, discernment, and classi cation. Alongside with the ISSR marker, which is a useful technique for allowing the identi cation of different selections and assessing the genetic similarity among studied pomegranate accessions, this would facilitate their use as identi ed genetic stock in future breeding programs.