Azadirachta indica was designated the "Tree of the 21st century" by the United Nations, as it is believed to be the largest natural depository of bioactive phytochemicals. This study investigates genetic variability among 152 Candidate Plus Trees (CPTs) of A. indica selected from three agro-climatic zones (ACZs) in eastern India: the Lower Gangetic Plains (ACZ III), Middle Gangetic Plains (ACZ IV), and the Eastern Plateau and Hills region (ACZ VII). Phenotypic characters, fruit and seed morphology, kernel oil content (KOC), and azadirachtin concentration (AC) were assessed to characterize the genetic diversity. Significant variation was observed across all parameters among individual CPTs. Girth at breast height ranged from 0.9 to 2.8 m, tree height from 6 to 16m, and crown volume from 146.95 to 2339.86 m³. Fruit length varied from 13.55 to 21.55 mm and seed length from 9.21 to 17.37 mm. KOC ranged from 36.51 to 58.86%, with a mean of 47.22% (±0.4), while AC showed extreme variability (19.46–1823.45 μg/g seed). KOC exhibited strong positive correlations with crown diameter (R=0.57, P≤0.001) and crown volume (R=0.45, P≤0.001). Interestingly, AC did not correlate significantly with any studied parameter, suggesting a high genotype×environment (G×E) interaction for this trait. Analysis of variance revealed significant differences (P<0.05) between ACZs, but only for some traits. Cluster analysis using Ward's minimum variance criterion based on Euclidean square (D²) distances performed in RStudio grouped the CPTs into five clusters as per pooled effects of all parameters. The highest inter-cluster distance was observed between clusters III and V (7.703), indicating a potential for heterosis in hybridization between these groups. Each cluster contained CPTs from all three ACZs, suggesting uniformly distributed variation across the study area rather than zone-specific patterns. This study provides valuable insights for improvement programs of the species and emphasizes the need for further research, including progeny trials, to comprehensively understand the genetic variability of A. indica in eastern India.