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Diseases caused by pathogens commonly occurring in the aquatic environment or those that are non‐host specific are prevalent and threaten the rapid growth of tropical aquaculture. This study investigates causes of mortality in 12 batches of newly stocked juvenile Lates calcarifer from three different hatcheries. Cytology based on Diff‐Quik™‐stained tissue and blood smears provides rapid diagnosis of possible causes of mortality, while histopathology and haematology provide a better understanding of how prolonged transport and fish with existing chronic disease are more likely to experience elevated mortality post‐stocking. Our findings showed that accumulation of ammonia during prolonged transport causes extensive damage to epithelial barriers in gastrointestinal tracts and depressed immunity due to marked hypoglycaemia, predisposing fish to acute Streptococcosis. Lates calcarifer with chronic bacterial enteritis developed severe hypoglycaemia, had low circulating total plasma protein, and suffered high mortality within 24 hours post‐stocking. Hypoglycaemia and low circulating blood proteins disrupt osmoregulation and exacerbate dehydration, which is fatal in fish in sea water. Dying L. calcarifer tested PCR positive for scale drop disease virus (SDDV) at 28 days post‐stocking showed a 10‐fold elevation of white blood cell counts, severe vasculitis, and obstruction of blood supply to major organs. Destruction of important immune organs such as spleen is a hallmark of SDDV infection that explains high incidences of opportunistic Vibrio harveyi infections in 61% of fish with SDDV. Overall, this study reiterates the importance of stocking disease‐free fish and reducing transport stress. [ABSTRACT FROM AUTHOR]

'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]