India has varied climatic conditions and recognised globally as megacentres of biological diversity. For conservation of biodiversity the DNA base markers provide valuable tool for assessing the genetic diversity. Phytochemical profiling establishes a characteristic phytochemical pattern for a plant material, its fraction or extracts. Both, molecular phylogenetic studies and studies of the phytochemical profile of higher plants have received considerable attention presently. The flora of Banasthali region has 47 trees, 48 herbs and 9 grasses. Among them Butea monosperma) is an economically important species with great medicinal value. However, B. monosperma has not been explored till date for its molecular profiling and chemoprofiling. The present attempt will focus on the authentication of wild medicinal plants of Banasthali region and chemo-molecular profiling of B. monosperma from different agroecological regions of India. It will also be of interest to know whether variations in the secondary metabolite level are correlated/ reflected in the pattern of molecular markers in Butea monosperma.