Abstract Cyprinid herpesvirus 2 (CyHV-2) is an emerging pathogen in the commercially exploited fish, Prussian carp (Carassius auratus gibelio), which has caused huge economic loss in China and appears to be spreading worldwide. In this article, CyHV-2 infection of Prussian carp was confirmed for the first time by polymerase chain reaction (PCR), which gave positive results from the tissue samples dissected from moribund fish including kidney, spleen, liver, and gill. Histological examination showed systemic inflammatory reactions in the infected tissues, with infiltration of hemocytes, hypertrophied nuclei, marginal chromatin and karyorrhexis, epithelial cell shedding, vacuolar degeneration and focal necrosis. Tissue alterations were also evaluated semi-quantitatively by the degree of tissue change. The values of degree of tissue change determined for kidney, spleen, liver, and gill were significantly greater than respective controls and kidney was the most severely damaged organ, with highest degree of tissue change value. In addition, a fluorescence in situ hybridization (FISH) based on oligonucleotide probes to detect the pathogen directly in the tissue, allowing pathogen–lesion correlation, was established. With the advantages of better tissue penetration, potentially more specific and stable, three oligonucleotide probes were designed. Positive reactions to the probes with intense green fluorescence were observed within the infected tissues where PCR and H&E analysis had suggested previously the presence of the virus within these lesions. The probes did not hybridize with host tissues of uninfected fish, nor did they cross-react with 3 other virus samples tested. The current research could facilitate the study of CyHV-2 infection mechanism in Prussian carp, and enhance the early diagnosis of the novel virus.