The genome sequence of the strain A/chicken/Changzhou/C08/2013 (H9N9) shows that the hemagglutinin (HA) genes of this strain are closely related to those of the strain A/chicken/Shanghai/1107/2013 (H9N2) and share 99.2% nucleotide homology, while the other seven genes had the greatest sequence identities with the novel H7N9 virus. We speculate that this strain may be a novel natural reassortant avian influenza virus (AIV).