Pharmacognosy has developed rapidly in recent years and now represents a highly interdisciplinary science. At the boundary between pharmacognosy and molecular biology, molecular pharmacognosy has developed as a new borderline discipline. Using the method and technology of molecular biology, molecular pharmacognosy focuses on resolving a wide range of challenging problems, such as distinguishing herbal and animal drug populations by molecular marker assay, conserving and utilizing wild resources on the basis of knowledge of genetic diversity, investigating the mechanism of active compound accumulation and obtaining new resources with higher quality through genetic engineering. Recent research results show that molecular pharmacognosy has extended the scope of pharmacognostical science and plays an important role in the safe and efficient usage of crude drugs.