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Santalum album L. is a commercially important tree that yields essential oil of high medicinal value. Regeneration research through organogenesis and embryogenesis has been documented but no report depicts comparative ontogeny of directly differentiating shoot buds (SB) and somatic embryos (SE). In the present study aseptic seedling derived hypocotyl segments (HC) and hypocotyl + root junction (HC + R) were used to induce SBs and SEs, respectively. Ontogenic differences between the structures were confirmed using scanning electron microscopy and histological analysis. MS medium con-taining 6-benzyladenine or BA (2.5 μM) produced highest number of direct SB, while MS + BA (7.5 μM) proved suitable for higher frequency of SE differentiation. The differentiating structures attained growth when transferred to MS medium containing a combination of BA and α-naphthalene acetic acid or silver nitrate (AgNO3). A combination of indole-3-butyric acid and silver nitrate (AgNO3) in half-strength woody plant medium and lesser osmotic concentration (2％ sucrose), induced rhizogenesis.