In the present paper, the authors introduce recent progress of application of molecular biological techniques in the studies on the underlying mechanism of acupuncture therapy for 1) resisting inflammation and relieving pain, 2) resisting tumors, 3) improving ischemic cerebral and myocardial injury, and 4) delaying aging from gene transcription and expression (synthesis of mRNA); and for relieving sciatic nerve injury, spinal traumatic injury, and cerebral ischemia from protein expression or phosphorylation. In addition, the authors also make a preliminary analysis on the extant problems of the application of techniques of both genomics and proteomics in acupuncture research at the present and predict their applicable prospect.