<p><i>Azadirachta indica</i> A. Juss. (neem) is a multipurpose tree species recognized for its ecological resilience and significant medicinal and economic utility. To support the increasing demand for high-quality neem-based products, the identification and selection of genetically diverse and morphologically superior genotypes is essential for the development of improved planting stock. The present study aimed to assess the genetic variability among 29 neem genotypes evaluated over three consecutive years (2018–2020) at three geographically distinct locations: Sagar, Amethi, and Kalol. Metroglyph analysis, a semi-graphical technique, was employed to characterize phenotypic diversity using ten traits, including four seed morphological traits (seed length, seed width, 100-seed weight, seed kernel ratio), two biochemical parameters (oil content and azadirachtin content), and four growth-related attributes (plant height, collar diameter, diameter at breast height, and number of branches). Cluster analysis based on seed and biochemical traits consistently classified genotypes into six groups across years, with some genotypes exhibiting temporal variation. Notably, genotype TN9 shifted from Group IV to V, indicating intermediate azadirachtin levels and moderate seed weight, while TN1 moved from Group VIII to VII, characterized by high azadirachtin content and lower seed weight. When growth traits were analyzed independently by location, genotypes at Sagar and Amethi formed six clusters each, whereas those at Kalol exhibited greater divergence, forming seven clusters. The results reveal substantial genetic diversity among the tested genotypes, highlighting the potential for selecting superior individuals for breeding programs. The study also demonstrates the utility of metroglyph analysis in effectively capturing trait-based diversity in tree improvement and forest genetic resource conservation initiatives.</p>