The invention discloses a molecular marker fingerprinting for identifying the anoectochilus formosanus produced at Huoshan in Anhui and the similar species thereof. The molecular marker fingerprinting comprises the steps of preprocessing anoectochilus formosanus samples, extracting DNA of each sample genome, executing ISSR-PCR (inter-simple sequence repeat-polymerase chain reaction), executing agarose gel electrophoresis, building ISSR molecular marker fingerprint of each sample and using the ISSR molecular marker fingerprint for identifying the anoectochilus formosanus germplasm. The method provided by the invention saves time and economic cost, and can obtain the accurate and reliable identification fingerprint just by extracting the DNA of the anoectochilus formosanus plants, executing ISSR-PCR and executing agarose gel electrophoresis; the method identifies the species, which are easy to confuse in appearance, from the essence of inheritance, has the advantages of being simple, convenient and efficient, excellent in repeatability and high in resolution, and so on; and the method can identify the species in seeding stage of plants, and plays an important role in guaranteeing the accuracy and the stability of the Huoshan anoectochilus formosanus crude drug base source.