Leaf samples of 40 Sandalwood (Santalum album L.) clones assembled at IWST, Bengaluru from natural growing areas and plantations in Tamil Nadu and Karnataka were analysed using horizontal starch gel electrophoresis to study isozyme variability for four enzyme systems: Peroxidase (POD), Aspartate amino transferase (AAT), Glutamate dehydrogenase (GDH) and Malate dehydrogenase (MDH). These systems are reported to show polymorphism in populations of Sandalwood in earlier studies. All the enzymes showed polymorphism in the present study. POD and MDH showing five and four different patterns differentiated the clones. Fourteen bands were scored with an average of 1.2 bands per clone. Presence of isozymes reflects the genetic complexity existing in the clones. No pattern of geographic distribution of isozyme variation was observed. The diversity observed among these clones would be useful in identifying diverse crosscombinations for deriving hybrids and establishing trials for production of seeds.