This paper proposed a noise filter with L2-norm distance method to design a classification of RNA sequences for the species identification, included of the small sample size of the nucleic acid sequence. This method amended and expanded the study by Hu et al. in 2011 . We verified this method with the biological sample "slipper orchids" and its hybrid for biological species identification test. The result is showed that after applied our method, we can distinguish the paternity of a hybrid among a set of samples of "slipper orchids".