H9N2 influenza viruses have become established in terrestrial poultry in recent two decades in different Asian countries. Our previous study demonstrated that quail harbor increasing diversity of novel H9N2 reassortants, including both Chicken/Beijing/1/94 (Ck/Bei-like) and Quail/Hong Kong/G1/97 (G1-like) viruses. However, since 1999 the genesis and evolution of H9N2 viruses in different types of poultry have not been systematically investigated. In the present study, H9N2 viruses isolated from chicken, duck and other minor poultry were genetically and antigenically characterized. Our findings demonstrate that Ck/Bei-like H9N2 viruses have been introduced into many different types of poultry including quail, partridge, chukkar, pheasant, Guinea fowl and domestic duck in southern China, while the G1-like viruses were commonly detected from quail, less frequently detected in other minor poultry and not detected in chicken and duck. Genetic analysis revealed 35 genotypes of H9N2 viruses, including 14 novel genotypes that have not been recognized before. Our results also suggested that two-way interspecies transmission exist between different types of poultry. Our study demonstrated that the long-term co-circulation of multiple virus lineages (e.g. H5N1 and H9N2 viruses) in different types of poultry have facilitated these frequent reassortment events that were mostly responsible for current great genetic diversity of H9N2 and H5N1 influenza viruses in this region. This situation favors the emergence of influenza viruses with pandemic potential.