Carassius auratus herpesvirus (CaHV) is a pathogen that can cause crucian carp disease with acute gill hemorrhages and high mortality. Interactions of functional genes with cellular components, such as cellular organs, are needed by viruses to complete infection and replication. In the present study, bioinformatic analysis, PCR amplification, gene cloning, constructing recombinant plasmids, and fluorescence observation of the fish cells (epithelioma papulosum Cyprinid, EPC) cotransfected with cellular organs tagged plasmids were used to analyze the characteristics, subcellular localization and colocalization with cellular organs of the protein encoded by the gene CaHV ORF31R (CaHV-31R). As the results show, the encoding protein CaHV-31R was composed of 313 amino acids, which consists of a transmembrane domain (248-270 aa) and a typical domain of RNase E/G protein family (40-182 aa). The multiple alignment with homology proteins from 5 different fish hepesviruses exhibited higher identity (100% and 80.7%) with the Janpanese strain ST-J1 and Chinese strain SY-C1, which were both the members of type Ⅱ Cyprinid hepesviruses, centered identity (26.5%) with CyHV-1 which was the representative member of type I Cyprinid hepesviruses, and the lowest identity (20.7% and 18.2%) with the Germanic strain CyHV-3(also named Koi herpesvirus, KHV) and Chinese strain (CyHV-3-GZ11), which were both the members of type Ⅲ Cyprinid hepesviruses. The plasmids pEGFP-31R was constructed by PCR amplification, gene cloning, and then used to transfect EPC cells. pEGFP-31R dispersed distribution in cytoplasm and a small part of spotty distribution were found circling around outside the nucleus. CaHV-31R was used to colocalize with two celluar organs with monolayer membrane in cytoplasm, which was endoplasmic reticulum and Golgi apparatus. The results indicated that CaHV-31R was a gene of Carassius auratus herpesvirus, and was able to encode a protein that colocalizes with cellular organs.