AbstractIn the marine aquaculture industry, photobacteriosis caused by the Photobacterium damselae subspecies piscicida, Phdp is a globally significant disease. A number of clinical photobacteriosis outbreaks among yearling cultured and broodstocks of gilthead sea bream were sampled and submitted to our laboratory during the summer and autumn of 2013. The tissues of infected fish were subjected to an ordinary bacteriological identification and were analyzed using the polymerase chain reaction (PCR) and immunohistochemistry techniques. The results indicated that the selective primers that have been designed for detecting the gene encoding the apoptotic‐induced protein, AIP56, represent a powerful tool for sensitive and specific detection of virulent strains of Phdp. AIP56 toxin triggers apoptosis of host macrophages and neutrophils, contributing to the lesions observed during the pathological investigation. Immunohistochemistry allows bacterial identification and antigen expression to be directly correlated to the disease; the immune‐positive bacteria were detected in gills, liver, kidneys, spleen, and brain tissues in acute photobacteriosis. These also appeared in the necrotic areas of the granulomas of chronically infected fish. Molecular and immunohistochemical methods were useful as research and diagnostic tools in different stages of the disease; moreover, they appear to have enormous potential in retrospective epidemiological investigations.