Lined seahorse, Hippocampus erectus, is an important aquatic animal due to its medicinal and ornamental purposes. However, our understanding of the viral spectrum in H. erectus is still limited. Here, we studied the viruses in H. erectus using meta-transcriptomic sequencing. A total of 213,770,166 reads were generated and assembled de novo into 539 virus-associated contigs. Three novel RNA viruses from the Astroviridae, Paramyxoviridae, and Picornaviridae families were finally identified. In addition, we identified a strain of nervous necrosis virus from H. erectus. In particular, the unhealthy group showed a higher viral diversity and abundance than the normal group. These results revealed the diversity and cross-species transmission of viruses in H. erectus and highlighted the threat of viral infections to H. erectus.