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A group of pathogenic nucleocytoplasmic large DNA viruses (NCLDVs) related to the Mimiviridae family infect farmed sturgeons across Europe, causing mild‐to‐severe losses. One of these viruses, Acipenser iridovirus‐European (AcIV‐E), was identified in six sturgeon species. During the 2018–2019 period, nine sick Siberian (A. baerii) and Russian (A. gueldenstaedtii) sturgeons were sampled in Ukrainian farms and tested for the presence of AcIV‐E using real‐time PCR. The presence of AcIV‐E was confirmed in some samples. High‐resolution melting (HRM) assay and Sanger sequencing demonstrated the presence in three farms of two alleles of the major capsid protein (MCP) gene, called var1 and var2. Five samples carried both var1 and var2 at varying ratios, and the sixth sample was infected with only var1. These results constitute the first detection of AcIV‐E in Ukraine and the first detection of a sample carrying only var1. The full‐length sequences of the MCP genes confirmed the existence of two genetic lineages of AcIV‐E, tentatively named V1 and V2, each displaying multiple substitutions in the MCP gene. Some of the MCP sequences showed a genetic relationship to both V1 and V2 lineages, depending on the fragment examined. Most likely, these sequences resulted from recombination events. [ABSTRACT FROM AUTHOR]