Ziziphus jujuba Mill is an important medicinal plant which is of high importance in medicinal industry due to containing mucilage, different types of vitamin, pectin, alkaloid, phenolic compounds and fatty acids. The current study was conducted to evaluate phylogenetic relations of jujube accessions using morphological, phytochemical and AFLP molecular markers. In morphological and phytochemical experiments, minimum, maximum, and average of fruit weight, were respectively 1.52, 2.99 and 2.31 g. In the same way, the minimum (1.3 g), maximum (2.65 g) and average (1.99 g) of fruit flesh weight were observed in accessions. The lowest (11.58 %) and highest (28.85 %) of mucilage quantity were related to Kalaghneshin1 and Kasva accessions. Simple correlation analysis of the traits showed that there were signifcant positive and negative correlations among some important traits including the positive correlation between the amount of mucilage and flesh to kernel ratio and kernel shape, and negative correlation between mucilage rate and kernel weight and diameter and fruit shape. Analysis of factors based on Varimax method defned four factors of fruit volume, kernel, fruit flesh and mucilage. Cluster analysis classifed accessions into four groups, and segregated three groups with Esfahani, Qomi and Mazandarani origins. In a similar matrix molecular experiment using Jaccard coeffcient, cluster analysis was performed by using UPGMA algorithm. 12 out of 15 pairs of AFLP primer showed polymorphism, with these primers producing 689 bands, out of which 44 bands presented polymorphism. Based on the results obtained from dendrogram, the studied accessions were divided into 8 discrete groups at similarity level of 0.75. AFLP marker could clearly cluster three groups of Qom, Esfahan and Khorasan. The results obtained from cluster analysis were confrmed by the principal component analysis. Two groups of Qom and Esfahan were distinctively separated in all markers; therefore these regions (central regions) can be introduced with high probability as one of the origins of jujube. In general, diversity of traits, effciency of markers and high correlation between the makers were considerable in segregation and separation of the accessions, and can provide an appropriate foundation for breeding of this valuable medicinal plant.
