Authenticating multi-species original raw materials in commercial formulations is difficult. Jin Yin Hua and Shan Yin Hua, both classified as raw honeysuckle materials in the Chinese Pharmacopoeia, are used in various medicines. Differentiating one variety from another is difficult based on chemical analysis. We developed molecular authentication of multi-species original honeysuckle in 3 brands of commercial tablets using allele-specific PCR. All 3 tablets contained both Jin Yin Hua and Shan Yin Hua. We also built a PCR-enzyme digestion method and enzymatic mutation detection in the PCR fragments of psbA-trnH and trnL-trnF, and the restriction endonucleases HinfI and NlaIV, respectively. The PCR-enzyme digestion method produced the same result as the allele-specific PCR. Sequence and phylogenetic analyses show that the tablets YXC and YQJ contained Lonicera japonica and L. macranthoides as original raw materials, and LYG contained L. japonica, L. hypoglauca, and L. macranthoides.