Introduction: The Atlas pistachio (Pistacia atlantica) is a robust tree endemic to North Africa with a well-defined trunk and deciduous leaves. It contributes to soil conservation and plays a vital role in reforestation programs in arid and semi-arid areas. Methods: This study focused on three populations of the Atlas pistachio tree located in different stations in the arid region of Algeria, namely: Sidi M'Hamed (M'sila), Messaad (Djelfa), and Ras El Miaad (Biskra). It was conducted to determine the morphological behavior of the species in arid bioclimatic regions, taking into consideration the effect of the soil physicochemical characteristics. In this regard, eleven traits of the trees, the leaves and the fruits were measured. Results: The statistical analysis of the soil physicochemical parameters concluded that the soils of the studied areas have a medium texture and moderately a basic pH, and are low to moderately limestone, slightly saline, and relatively rich with the organic matter. Regarding the morphological variability, groups of stations were discriminated based on the different variables studied. The principal component analysis (PCA) revealed a correlation between the dimensions of the trees and the leaves with the soil properties and the climatic factors. It allowed dividing the three stations into three groups. The variables of total tree height, tree circumference, crown height, organic matter, soil moisture content, pH, electrical conductivity, total limestone content, and altitude discriminate the station SM (group 1). The variables fruit length, leaf area, leaf width, and leaf length discriminate the station MS (group 2). The station RM represents group 3 and is characterized with the variables of trunk height and fruit width.