Viral infections pose a significant challenge to modern aquaculture. Among these, koi herpesvirus disease (KHVD) causes significant economic losses in carp aquaculture. KHVD is a highly contagious and emerging disease that causes significant mortality in common carp and koi. It is caused by Cyprinid herpesvirus 3 (CyHV-3), commonly known as “koi herpesvirus.” The World Organization for Animal Health has classified KHVD as a notifiable infectious disease since 2007, emphasizing the need for early detection and reporting to facilitate effective disease management. This study aimed to detect KHVD at the molecular level and conduct a histopathological examination of suspected carp farm mortalities in the Susangerd region (Khuzestan, Iran). Gill tissue samples were collected from infected fish at affected farms, followed by molecular assays and pathological analyses to identify CyHV-3. This study represents the first confirmed detection of KHV in carp farm mortalities in the region using clinical, histopathological, and molecular investigations. Clinically, infected fish exhibited lethargy, erratic swimming, congregation on the surface of the water, movement along the pond’s perimeter, frequent gasping for air, occasional excessive mucus production on the skin, and sunken eyes before death. The histopathological analysis revealed gill tissue abnormalities, including hyperplasia, congestion, and intranuclear inclusions with chromatin margination. Additionally, the sequence analysis of the polymerase chain reaction (PCR) product confirmed CyHV-3 as the causative agent of these mortalities. The sequenced viral product was submitted to GenBank under accession number PQ120584.