Potential single nucleotide polymorphisms (SNPs) of FNSII gene is helpful to identify Lonicera japonica and Lonicera confuse. Previously, 12 samples had been identified into five Lonicera species (Lonicera japonica Thunb., Lonicera macranthoides Hand.–Mazz., Lonicera hypoglauca Miq., Lonicera fulvotomentosa, Lonicera confusa) in the base of base resource. Here, we have performed further study on these 12 samples. First, homology–based cloning was employed to clone their FNSII genes, and then SNP analysis. To our knowledge, our study is the first time to obtain the FNSII gene sequences from Lonicera hypoglauca Miq., Lonicera fulvotomentosa and Lonicera confusa. The similarity of all the cloned 20 FNSII gene fragments is over 95%, the phylogenetic analysis shows that genetic relationship of these Lonicera L. is consistent with the identification results. 38 SNPs were identified from 20 sequences in 12 samples via sequence alignment. According to the difference of SNPs, all samples can be classed into 5 genotypes according to the total 38 SNPs, which were identified from 20 sequences cloned in 12 samples and 19 of which can be used for the species indenfication.