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'Big belly' disease is a chronic, granulomatous bacterial enteritis and peritonitis, first reported in 3‐ to 4‐week‐old Asian seabass or barramundi, Lates calcarifer Bloch fry. Affected fry are emaciated and have a swollen abdomen, and the condition is referred to as 'skinny pot‐belly' or 'big belly' disease. In this study, histopathological examinations of diseased fish from a batch of 2‐month‐old, 6‐ to 8‐cm L. calcarifer fingerlings, kept in seawater recirculating aquaculture systems, showed pathology resembling 'big belly' disease. Ethanol‐fixed tissues were tested positive using specific PCR primers based on 16S rRNA genes. In situ hybridization using dioxygenin‐labelled positive PCR products on formalin‐fixed paraffin‐embedded tissues showed positive reactions with intralesional, clusters of the large, 'big belly' coccobacilli. A phylogenetic tree constructed based on analyses of these 16S rRNA gene PCR products from five positive fish suggests that the 'big belly' bacterium is most likely a novel Vibrio species. [ABSTRACT FROM AUTHOR]