ABSTRACT Infectious spleen and kidney necrosis virus (ISKNV), a member of the species Megalocytivirus pagrus1 , poses a significant threat to global aquaculture and has recently emerged as a major pathogen in farmed tilapia. This study reports the identification and characterisation of an ISKNV strain, designated ISKNV‐VS456, isolated from a lethal outbreak in Indonesian farmed tilapia. A Nile tilapia challenge experiment confirmed the virus's high pathogenicity, causing 100% mortality by 10 days post‐infection (dpi), with the kidney identified as a key site of viral replication. Infected fish exhibited clinical signs such as edema, skin haemorrhages, and organ haemorrhages, while histopathological analysis showed extensive damage in the kidney and spleen. The whole genome of ISKNV‐VS456 is 111,605 bp long, containing 124 open reading frames, consistent with a typical ISKNV genome. Several virulence‐related genes were detected, including ORF022L , ORF069L , ORF071L , ORF103R , and ORF111L . Phylogenetic analysis of the major capsid protein ( mcp ) gene placed ISKNV‐VS456 within the ISKNV‐I subgenotype, which is associated with high virulence in tilapia. This study provides the first whole‐genome sequence of a lethal Megalocytivirus pagrus1 strain ISKNV‐VS456 from Indonesian farmed tilapia ( Oreochromis niloticus ) in Indonesia, contributing to a better understanding of the virus in Southeast Asia, where the disease is most severe.