Avian influenza virus A/chicken/Jiangsu/1001/2013(H5N2) was identified from a healthy chicken in an eastern China poultry market. Whole-genome analysis demonstrated that the H5N2 virus originated from a reassortance between a previous A/chicken/Hebei/1102/2010(H5N2) virus and an endemic H5N1 virus. The results indicated that continuing reassortance of H5N2 has been occurring in domestic poultry of China.