We analyzed the results from nationwide surveillance of avian influenza (AI) from birds in South Korea's major wild bird habitats and the demilitarized zone of South Korea, 2003–2008. Of 28,214 fecal samples analyzed, 225 yielded influenza viruses, for a prevalence of 0.8%. Hemagglutinin (HA) subtypes H1–H12 and all nine neuraminidase (NA) subtypes were detected. The dominant HA subtypes were H6, H1, and H4, and the most common NA subtypes were N2, N1, and N6. Among the 38 HA/NA subtype combinations, the most common were H4N6, H6N1, and H5N2. Thirty-seven low-pathogenic AI (LPAI) viruses of the H5 and H7 subtype were detected. Among them, we identified bird species for 16 H5- and H7-positive fecal samples using a DNA bar-coding system instituted in 2007; all birds were identified as Anseriformes. The HA gene of the H5 wild bird isolates belonged to the Eurasian avian lineage, and could be clearly distinguished from the sublineage H5N1 highly pathogenic AI (HPAI) of the Eurasian and American avian lineages. Whereas H7 LPAI viruses did not group as a separate sublineage with H7 HPAI viruses, H7 isolates were closely related with the Eurasian avian lineage.