Most wild species and wild relatives of banana (Musa spp.) are found in forests and are thus relatively inaccessible. Their inability to establish in places different from their natural habitats further complicates the use of such wild species for routine molecular research. The present study was therefore undertaken to evaluate seeds as an alternative source of DNA for conservation in comparison with the cigar leaf. Usefulness of seed as a major genetic tool for conservation of seeded wild banana germplasm, standardisation of the stage of seed maturity for DNA extraction and standardisation of the seed DNA extraction protocol were studied. The accessibility of seed DNA as an alternative strategy for leaf DNA was confirmed using molecular markers (RAPD and IRAP). Among different methods of DNA extraction, a modified protocol with cetyltrimethyl ammonium bromide (CTAB) was found to be the best. Partially mature seeds with 70-80% maturity were found to be the best stage for DNA extraction compared to 40-50% and 100% maturity. Removal of the seed coat improved the quality of DNA extracted. Uniformity of seed and leaf DNA was confirmed by using 80 random primers and 10 IRAP primers. The paper tries to analyse the extent of deviation between seed and leaf DNA and possible reasons in view of the breeding behaviour of wild species.