Salvia fruticosa Mill. is a high-value aromatic perennial widely utilized in the pharmaceutical and food industries due to its potent essential oil profile and secondary metabolites. Despite its economic importance, the influence of environmental gradients on the physical seed characteristics of wild populations remains poorly understood. This study aimed to characterize the morphological and physical attributes of S. fruticosa seeds collected from 25 distinct wild populations across Denizli province, Türkiye, and to evaluate the impact of altitude and topographical factors on these traits. Physical parameters, including length, width, thickness, geometric mean diameter, sphericity, surface area, and thousand-seed weight, were systematically measured. Statistical analysis revealed significant morphological divergence among locations (P<0.05). Seed length and width ranged from 1.70 to 2.50 mm and 1.13 to 1.92 mm, respectively, while thousand-seed weight exhibited substantial variation between 4.07 g and 11.26 g. Principal Component Analysis (PCA) accounted for 88.4% of the total variance, identifying a robust positive correlation between seed dimensions and mass, while sphericity remained relatively independent. The results demonstrated that altitudinal gradients and aspect significantly influence seed quality, with higher elevations generally exerting a negative impact on seed dimensions and mass. Populations from lower altitudes and favorable microclimates exhibited superior physical traits. These findings highlight the extensive phenotypic diversity within Denizli’s wild germplasm, providing a critical foundation for the selection of superior genotypes and the optimization of post-harvest processing in future breeding programs.