Abstract: A method for species identification by using molecular weights of nucleic acid cleavage fragments, comprising steps of: performing a polymerase chain reaction and a nucleic acid cleavage reaction to cleave the nucleic acid sequence of the to-be-identified species into multiple nucleic acid cleavage fragments having different molecular weights; measuring the molecular weights of the nucleic acid cleavage fragments by using a mass spectrometer; comparing the molecular weight of each nucleic acid cleavage fragments of the to-be-identified species with molecular weights of nucleic acid cleavage fragments of a known species in a database; determining a number N of the identical nucleic acid cleavage fragments between the two species; and calculating a ratio N/M of the number N to the total number M of the nucleic acid cleavage fragments of the known species, wherein the ratio N/M represents similarity between the to-be-identified species and the known species.