Seed and seedling traits govern plant fitness and persistence and are influenced by the interaction between the plant and its environment. Changing climatic and edaphic conditions will drastically affect early fitnessrelated traits and can alter the demography and species distribution range. It is widely documented that trait variation among populations may increase resilience of tree communities and reduce the risk of extinction under future climates. In the present study, variation in seed and seedling traits were documented from seven populations of Santalum album representing the natural distribution range of the species in the Indian subcontinent. Significant intra-specific variation was documented in seed and seedling traits, indicating high adaptive potential of the species. Further, the measured traits were correlated with climatic variables. No significant correlation was predicted for seed-related traits, while seedling-related traits like shoot and root weight, photochemical reflectance index, relative water content, and root-shoot ratio correlated with different climatic parameters. Variance partitioning revealed predominant combined effect of environment and genotype on seed traits except seed weight, which was governed by genotypic effect. The dominance of genotypic effect was documented for all seed leachate parameters, while seedling-related traits were predominantly affected by the environment. Conservation of sandalwood genetic resources will benefit from the insights gained from the variability recorded in these fitness-related traits, which are likely to affect the adaptive potential of the species.