Synthetic seed has become a proficient tool that facilitates conservation as well as mass propagation of elite plant species by encapsulating somatic embryo or meristem tissue. Inclusion of meristematic tissues instead of somatic embryos hastens widespread utilization of this technology in recent years. Synseeds offer short term conservation of germplasms, provide readily available tissue source for easy mass propagation where each synseeds can virtually act as zygotic seeds giving rise to plantlets. This is the first report on synseed production following the confirmation of the genetic homogeneity in regenerated plantlets of Balanites aegyptiaca Del. (L.) using ISSR marker system. In this study, nodal segments, excised from in vitro proliferated shoot cultures developed from mother plant, were encapsulated in calcium alginate beads and the finest gel complexation was achieved using 3 % sodium alginate and 100 mM CaCl 2 ·2H 2 O. Maximum percent response (80 %) for conversion of encapsulated nodal segments into plantlets was obtained on Murashige and Skoog (MS) medium containing 12.5 μM benzyladenine and 1.0 μM α-naphthalene acetic acid. Encapsulated nodal segments could be stored at low temperature (4 °C) up to 4 weeks with a survival frequency of 82 %. The regenerated shoots were rooted on half strength MS medium augmented with 1.0 μM indole-3-butyric acid. Well-developed plantlets regenerated from encapsulated nodal segments were acclimatized successfully with 90 % survival frequency. Fingerprinting profiles of the regenerated plantlets derived from synseeds and the donor plant were generated using a total of 20 ISSR primers, of which 14 primers produced distinct, reproducible amplified products. A total of 158 scorable bands were obtained from the complete amalgamation of primers and plantlets and 98.7 % bands were monomorphic across the plantlets which indicate that this micropropagated line derived from synseed is genetically stable and demonstrates the reliability of our protocol for short term conservation, germplasm exchange and distribution of identical plants.