Analysis of genetic diversity and population structure of Santalum album genotypes revealed moderate genetic variability and differentiation across 14 populations from three Indian states. Data derived from both genomic and genic SSR markers provided precise insights into the distribution of genetic diversity within these populations. The observed genetic variation offers valuable information for selecting elite genotypes that can be used in genetic improvement, conservation management, and tree breeding programs. Furthermore, these markers serve as effective tools for investigating genetic diversity and the population structure of S. album in natural and cultivated populations across other states. The molecular markers developed in this study demonstrated adequate levels of polymorphism across loci, enabling further analysis of genetic diversity, differentiation, and population structure in S. album. These findings have the potential to significantly advance sandalwood genetics and breeding programs, particularly in identifying elite germplasm and facilitating marker-assisted selection.