Assessment of genetic diversity and relationship among six landraces of jackfruit (Artocarpus heterophyllus) grown in Aswan Botanical Garden (Aswan, Egypt) was preformed using morphological, chemical and molecular evaluations. A wide range of variability was observed among the tested landraces, reflected by highly significant differences in all evaluated traits. Among which, fruit length, seed weight, fruit peel weight, total phenolics, non-reducing sugars, protein, calcium, phosphorus and potassium content showed higher influence than others, the way that affected the relationship among landraces and their grouping in dendrogram. These traits are highly recommended to be included in successive evaluation studies of jackfruit. Cluster analysis based on the phenotypic data allowed the grouping of the landraces according to their shared features of higher or lower values of morphological and chemical traits, which could be helpful in the subsequent crop improvement efforts. On the other hand, molecular analysis using inter simple sequence repeats (ISSR) markers clearly confirmed the degree of variability among jackfruit landraces by showing a high percentage of polymorphism (up to 71.43%) and providing a good cluster relationship in the ISSR-based-dendrogram. Furthermore, combining phenotypic and molecular data to perform cluster analysis, gave an insight into the landraces' relationships. High similarity was observed between molecular- and combined-based dendrograms unlike phenotypic-based one. Results herein can benefit the breeding programs of jackfruit.