Seahorses (genus Hippocampus) are flagship species for marine conservation and evolutionary studies.Wild seahorse populations have declined sharply because of overfishing or other disrupting activities, which are attracting increasing global concern for their threatened status.For study of their population status, the identification of young seahorses by morphological examination has been controversial and remains a difficult task due to overlapping of meristic and morphological characters.Here we reported a simple and sensitive method to identify seahorse species from China based on cross-species microsatellites.