"Ephedra" is a gymnospermic genus of Gnetales and family Ephedraceae. The genus is represented by forty-two species from the world, among them nine are provisionally reported from Pakistan. It is recognized for fourteen phyto-chemicals, among them ephedrine and pseudo-ephedrine are the most important, widely used as bronchodilators and decongestants. Traditionally the plant is used for respiratory tract diseases and to enhance the effect of snuff. Besides its use as medicine, some of its species are used as diet supplement for weight reduction. Quantity and quality of chemicals present in the genus vary species to species. Hence, it is important to properly identify the plant and get benefit from its valuable chemicals. Conventional tools of taxonomy can identify the genus but overlapping morphological features of the plant creates problems in proper alignment of species. PCR based Molecular markers e.g. RAPDs can help to delineate various field specimens with high accuracy and thus provide a handy tool for identification.