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The phylogenetic relationships of 90 wild grown Capparis spinosa genotypes which are collected from nine sampling sites from three valleys viz. Suru (3,309 m above mean sea level [amsl]), Nubra (2,926 m amsl) and Indus (3,505 m amsl) of trans-Himalayan region were analyzed using 40 PCR markers (20 random amplified polymorphic DNAs [RAPDs] and 20 inter simple sequence repeats [ISSRs]). RAPD analysis yielded 223 fragments, of which 220 were polymorphic while, ISSR produced 85 bands, of which all are found polymorphic, with an average of 11.0 and 10.62 polymorphic fragments per primer respectively. ISSR markers were found more efficient in relation to polymorphism detection. Clustering of individuals within groups was not similar when RAPD and ISSR derived dendrogram were compared, whereas the pattern of clustering of the individuals remained more or less the same in RAPD and combined data of RAPD + ISSR. analysis of molecular variance analysis showed that total variation within the population was maximum, followed by among population and least for among valley in all the three cases. Pertaining to the management of caper, the high genetic differentiation of population indicated the requisite of conserving the utmost possible number of populations from different valleys of trans-Himalayas.