Herbal drug technology is used for converting botanical materials into medicines, where standardization and quality control with proper integration of modern scientific techniques and traditional knowledge is important. The use of chromatographic techniques and marker compounds to standardize botanical preparations has limitations because of their variable sources and chemical complexity. DNA-based molecular markers have utility in the fields like taxonomy, physiology, embryology, genetics, etc. DNA-based techniques have been widely used for authentication of plant species of medicinal importance. Pharmacognosy mainly addresses quality-related issues using routine botanical and organoleptic parameters of crude drugs, and chemoprofiling-assisted characterization with chromatographic and spectroscopic techniques. The new pharmacognosy includes all the aspects of drug development and discovery, where biotechnology-driven applications play an important role. Current focus on chemotype-driven fingerprinting and related techniques requires integration with genotype-driven molecular techniques so that an optimal characterization of botanical materials is possible. This review provides a brief account of various DNA-based technologies that are useful in genotyping and quick identification of botanicals with suitable examples.