Background: Corynosoma is a parasite from the Acanthocephala phylum with worldwide distribution. Corynosoma parasites are found in pinnipeds as their definitive host. Aims: This study aimed to investigate the morphological and molecular characteristics of Corynosoma, and its histopathological effect on the intestinal tissue of Pusa caspica. Methods: A severe Corynosoma infection was observed in the small intestine of a juvenile male Caspian seal (P. caspica). The morphological descriptions were done using light microscopy, and scanning electron microscopy (SEM). The molecular diagnosis was performed using partial sequences of internal transcribed spacer 1 (ITS1) and 5.8S ribosomal RNA (rRNA) gene. Results: According to the results, the Corynosoma specimens were identified as Corynosoma caspicum. The histopathological inspection of intestinal tissue revealed lesions in epithelial cells, mucosa, submucosa and muscle layers, destruction of intestinal glands, and infiltration of inflammatory cells. Conclusion: Presence of such a severe infection in one of the individual Caspian seals can suggest the possibility of morbidity among other seals in the landlocked Caspian Sea. Thus, further research on their parasite infections is required for understating the status of the Caspian seal population and conserving this endangered species.