The invention discloses a SSR molecular marker method for identifying two hippocampus populations. EST (Expressed Sequence Tag) sequences of Japanese hippocampus and hippocampus trimaculatus are utilized to design six pairs of SSR molecular marker primers in total, respectively including (i)Hmo(/i)48, (i)Hmo421(/i), (i)Hmo(/i)242, (i)Hmo(/i)244, (i)Htr(/i)6 and (i)Htr(/i)8, wherein the (i)Hmo(/i)242 and the (i)Hmo(/i)244 belong to shared primers of the Japanese hippocampus and the hippocampus trimaculatus; the (i)Hmo(/i)48 and the (i)Hmo421(/i) belong to specific primers of the Japanese hippocampus; the (i)Htr(/i)6 and the (i)Htr(/i)8 belong to the specific primers of the hippocampus trimaculatus. DNA (Deoxyribonucleic Acid) of the hippocampus is extracted and subjected to a treatment of PCR (Polymerase Chain Reaction) amplification by utilizing the primers. The primers disclosed by the invention have an extremely-high specificity and an extremely-high stability between the two hippocampus populations, therefore a PCR product is subjected to normal agarose gel electrophoresis detection so that the hippocampus population can be rapidly judged, and a reference is provided for genetic diversity protection and fine breed introduction of the hippocampus.