Aravallis, one of the oldest mountain systems in world is rich in plant resources including medicinal and aromatic plants. Due to biotic and abiotic pressures compounded by poor natural regeneration have made certain species threatened requiring immediate attention for conservation. They include Boswellia serrata, Feronia limonia, Celastrus paniculatus and Chlorophytum borivilianum. The present study therefore, was aimed to assess genetic structure of the natural populations of these species using DNA based molecular markers such as RAPD and ISSRs. Molecular evaluation of in vitro derived clones was also carried out to ensure clonal fidelity in micro-clones developed as a part of ex situ conservation strategy. Molecular analysis of all the four plant species yielded interesting data. In case of B. serrata no genetic variation was observed within the populations as revealed by RAPD and ISSR profiles. Analysis of data using various tool-sets reflected low gene flow among populations. However, in F. limonia the ISSR profiles revealed low but very significant amount of gene flow among the populations. Analysis of RAPD and ISSR profiles of C. borivilianum suggested significant diversity within 14 wild populations which could be clustered into 8 groups. Molecular screening of in vitro derived clones expressed absolute fidelity in F. limonia, C. paniculatus and C. borivilianum, irrespective of mode of regeneration and marker system used.