The Goose/Guangdong lineage highly pathogenic avian influenza (HPAI) clade 2.3.4.4 viruses have spilled over to wild birds and caused transboundary epizootics. In 2016, the H5N6 subtype of clade 2.3.4.4 HPAI viruses was introduced to Korea and Japan by wild waterfowls. However, the detailed geographic location of the origin of this outbreak was not fully defined yet. In this study, the geographical origin of this outbreak was estimated using phylogeographic analysis. The results indicate that the H5N6 viruses of wild birds originated from a virus in Guangdong province, China. In addition, Guangdong province was an epicenter for H5N6 viruses, and multiple spillovers of viruses from poultry into wild birds have been detected. Thus, to predict and prepare for the next HPAI outbreak in Korea and Japan, viruses in Guangdong province should be carefully monitored and investigated.