9Boswellia serrata, an economically important indigenous tree of dry deciduous forests, provides 10 oleoresin gum of pharmaceutical significance and excellent pulp for paper industries, but faces 11 threat to extinction due to poor natural regeneration and commercial exploitation. 240 12 individuals of the species representing 12 locations of its natural distribution in central India 13 were investigated to compare the genetic differentiation indices, Q ST for GBH and wood fiber 14 length and ϕ ST for neutral (RAPD+ISSR) markers. The comparison for paired locations was more 15 informative than for metapopulation. The most paired locations were either under the stabilizing 16 selection (Q ST (L) < ɸ ST (L)) or in the genetic drift (Q ST (L) = ɸ ST (L)) whereas a relatively small 17 number of paired locations was under the divergent selection (Q S T (L) > ɸ ST (L)). The 18 comparison for the metapopulation generating only a single trend of Q ST (P) > ɸ ST (P) is, 19 therefore, misleading. For conservation, the genetically deficit locations (Q ST (L) < ɸ ST (L) and 20 Q ST (L) = ɸ ST (L)) of B. serrata warrant for reinforcement of their genetic diversity by 21 introduction of genotypes from other genetically divergent locations (Q ST (L) > ɸ ST (L)), which 22 would check the fragmentation and genetic drift, resulting in reproductive vigour, natural 23 regeneration and reverse the endangered status of the species.24