Live bird markets (LBMs) provide an ideal environment for the evolution and interspecies transfer of avian influenza viruses (AIVs). In this study, we analyzed AIVs present in LBMs in Korea during the winter seasons of 2006–08. Sixty-five AIVs that belong to four hemagglutination (HA) subtypes of AIV (H3, H4, H6, and H9) were isolated from 644 pooled tissue or swab samples collected in LBMs. Most H9 subtypes of AIVs were isolated from Galliformes (chickens, silky fowls, pheasants, and guinea fowls), and other subtypes were isolated from Anseriformes (Pekin ducks and mallards). In addition, we obtained a single H3N2 virus from nasal swabs of dogs sold in LBMs, and the virus was genetically identical to the canine influenza virus (CIV) isolated from pet dogs in Korea. Phylogenetic analysis suggests that the Korean H9N2 viruses prevalent in chickens have provided their gene segments to AIVs circulating in ducks. These gene transfers facilitated reassortment events among AIVs and likely generated the ancestors of CIV in Korea. An animal challenge study using chickens, quail, mice, and dogs had shown that the H4 and H6 subtypes could replicate in mice and that some H4 and H6 viruses could replicate in chickens without preadaptation. In addition, two H3 subtype viruses (H3N2 and H3N8) induced interstitial pneumonia that accompanied clinical signs and seroconversion in dogs. Our findings indicate that the newly evolved AIVs have been continuously generated by reassortment in ducks, and these reassortments could result in expanding the host range of AIVs.