AbstractThe codon usage patterns of open reading frames (ORFs) in cyprinid herpesvirus 3 (CyHV‐3) have been investigated in this study. The high correlation between GC12% and GC3% suggests that mutational pressure rather than natural selection is the main factor that determines the codon usage and base component in the CyHV‐3, while mutational pressure effect results from the high correlation between GC3% and the first principal axis of principle component analysis (Axis 1) on the relative synonymous codon usage (RSCU) value of the viral functional genes. However, the interaction between the absolute codon usage bias and GC3% suggests that other selections take part in the formation of codon usage, except for the mutational pressure. It is noted that the similarity degree of codon usage between the CyHV‐3 and goldfish, Carassius auratus (L.), is higher than that between the virus and common carp, Cyprinus carpio L., suggesting that the goldfish plays a more important role than the common carp in codon usage pattern of the CyHV‐3. The study of codon usage in CyHV‐3 can provide some evidence about the molecular evolution of the virus. It can also enrich our understanding about the relationship between the CyHV‐3 and its hosts by analysing their codon usage patterns.