To establish a rapid and accurate allele-specific diagnostic Polymerase Chain Reaction (PCR) method for Syngnathus.TheSyngnathus genomic DNA were extracted and bidirectionally sequenced.Then the sequences were analysed.On this basis, specific identification primers were designed according to the sequences of specific alleles.PCR reaction system was established and optimized in this study.Genetic distance analysis of six species of Syngnathus samples showed that variation of intraspecific and interspecific genetic distances were: 0.00%-0.31% and 7.47%-27.08%, the average interspecific genetic distance was far higher than the average intraspecific genetic distance.Phylogenetic tree shows that six species of Syngnathus were strictly clustered as a single system individually.For the optimization, in 20 μL PCR reaction system, the template DNA sample volume was in a range of 5-100 ng, the annealing temperature was feasible from 43 ℃-55℃, the authentic samples of Syngnathoides biaculeatus, Solenognathus hardwickii, Syngnathus acus were amplified with a single and clear band which were 240 bp, 318 bp, 139 bp individually by the specific identification primers HLN, HLD, HLJ.The identification system was specific and stabilized, multi-source Syngnathus samples can be quickly and accurately identified.