The invention discloses a method for identifying molecules of epimedium sagittatum and epimedium myrianthum. The method comprises the following steps of (1) extracting DNA (deoxyribonucleic acid) of ato-be-tested sample; (2) using the DNA of the to-be-tested sample as a template, and performing PCR (polymerase chain reaction) amplification on a segment containing chloroplast psbA-trnH sequence; (3) splicing the amplified products, so as to obtain the complete chloroplast psbA-trnH sequence; (4) establishing a system development tree with sequenced and spliced psbA-trnH sequence based on a K2Pmodel. The method has the advantages that the suitability is strong, the operation is simple, the epimedium sagittatum and the epimedium myrianthum can be quickly and accurately identified, and a large amount of samples can be identified in short time.