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The application of different methods to assess genetic diversity is crucial for plant breeding and conservation programs. In this study, the morphological traits, the biochemical parameters and 11 ISSR molecular marker were used to investigate 11 Moroccan walnut accessions. The results of the morphological study revealed an important variation of the analyzed traits. The largest variation revealed in the position of the pad on the suture (CV=45.02%), whereas for leaflet margin no variation was found. The matrix of the Euclidean distance coefficient exhibited a large morphological variation between accessions, ranging from 3.1 to 12.1. In addition, the Mantel test showed no correlation between morphological and geographical distance of the accessions (r=0.159, p=0.84). Regarding the biochemical results, the parameters revealed a large variation. The coefficient of variation of energy value was the lowest (3.68%) while that of total flavonoids was the highest (62.02%). For the molecular analysis, the results indicated a high percentage of polymorphism (89%) as well as efficiency of the primers UBC836 and UBC841 in the research of the genetic diversity of this species. The principal component analysis divided the 66 trees into three groups independently of geographic origin and mountain range type. In addition, the altitude provided a weak effect on the structuring of the accessions (1.8%). Finally, the mantel test showed no significant correlation between the molecular and morphological markers (r= 0.591; P value= 0.998), molecular and biochemical markers (r=0.38; P=0.475), and morphological and biochemical markers (r=0.602, P=0.784). The results of this work can be useful for the conservation and improvement program of walnut in Morocco. [ABSTRACT FROM AUTHOR]