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At the boundary between pharmacognosy and molecular biology, molecular pharmacognosy has developed as a new borderline discipline. This paper reviews the methods, application, and prospect of molecular pharmacognosy. DNA marker is one of genetic markers and some molecular marker methods which have been successfully used for genetic diversity identification and new medicinal resources development. Recombinant DNA technology provides a powerful tool that enables scientists to engineer DNA sequences. Gene chip technique could be used in determination of gene expression profiles, analyses of polymorphisms, construction of genomic library, analysis of mapping, and sequencing by hybridization. Using the methods and theory of molecular biology and pharmacognosy, molecular pharmacognosy represents an extremely prospective branch of pharmacognosy and focuses on the study of systemic growth of medicinal plants, identification and evaluation of germplasm resources, plant metabolomics and production of active compounds. Furthermore, the great breakthrough of molecular pharmacognosy could be anticipated on DNA fingerprint analysis, cultivar improvement, DNA identification, and a global DNA barcoding system in the future.