The aim of the investigation is to achieve molecular characterization of the medicinal plant Citrullus colocynthis through short orthologous DNA marker. The molecular characterization of Citrullus colocynthis is performed by following standard protocols for DNA barcoding specific to Angiogerms based on trnH-psbA intergenic spacer region. The method initially begins with plant sample collection followed by Doyle and Doyle method of DNA isolation, PCR amplification and DNA sequencing. The short sequence obtained was also analyzed insilico using Blastn and Portable software for Molecular Evolutionary Genetics Analysis (MEGA version 6). The DNA sequence of Citrullus colocynthis trnH-psbA intergenic spacer region was 181 base pair long. The Blastn sequence analysis found an array of 13 homologous eudicot species. The evolutionary divergence analysis based on maximumlikelihood (ML) phylogenetic tree and pairwise distance Matrix revealed closely related species and Ancestral data.
