To study the germplasm resources and genetic diversity of the wild population of Hippocampus japonicus, the mitochondrial DNA control region fragments were obtained from wild populations by PCR amplification. The homologous sequences of other Syngnathidae fishes from GenBank were also included in this study. PCR amplification products of 557–558 bp CR fragments were obtained, and the average contents of A, T, G and C were 34.3%, 29.7%, 14.1%, 21.9%, respectively. A total of 16 polymorphic nucleotide sites were detected, which defined 16 haplotypes. The variation level was low as H was 0.70±0.02 and π was 0.0032±0.0021. With the aid of the homologous sequences retrieved from GenBank, phylogenetic trees were constructed based on neibour-joining (NJ), maximum-likelihood (ML) and Bayesian inference (BI) methods to build phylogenetic relationships within the Syngnathidae fishes. The phylogenic analysis showed that the topology of phylogenetic trees were almost consistent with each other, although the NJ tree and the ML/BI tree were somewhat different. The phylogenic analyses of CR gene sequences were also consistent with morphological taxonomy. Based on the results, several conclusions were drawn as follows: (1) CR is an appropriate marker for the seahorse species identification and population genetic analysis; (2) CR is highly divergent among different Syngnathidae fishes and could be an appropriate marker for molecular systematic studies. This study is expected to provide important information for the protection and utilization of H. japonicus resources in China.