Avian influenza virus (AIV) subtype H9N2 is greatly threatening to Pakistan poultry, even with stringent vaccination policies. Subtype H9N2 avian influenza viruses (AIV) continues to cause significant outbreaks in commercial and backyard poultry in Pakistan. Subsequently, subtype H9N2 AIVs are occasionally reported from humans, widespread incidence of H9N2 in poultry and non-poultry avian species executes a great risk for public health. Until now, the genetic evolution of H9N2 viruses in various host organisms in Pakistan has not been thoroughly investigated. However, this is the primarily report of isolation of low pathogenic AIV in non-poultry avian species including ducks, black swan, peacock and pheasants in Pakistan. The study has been carried in National Zoos and live birds market (LBM) situated in Lahore district and commercial and backyard poultry in Kasure, Gujranwala, Sheikhpura and Sialkot districts of Punjab province and Bhimber, Kotli and Mirpur districts of Azad and Jammu Kashmir (AJK). In the present study, twelve low pathogenic avian influenza viruses (LPAIVs) subtype H9N2 isolated from clinically healthy and diseased ducks, geese, black swans, pheasants and peacocks and five from poultry outbreaks during 2016-17 were characterized phylogenetically on the basis of hemagglutinin (HA) and neuraminidase (NA) genes. Phylogenetic studies showed that these H9N2 AIVs belonged to Middle East B genetic group of G1 sub-lineage. All the viruses carried an amino acid substitution Q226L in HA gene in the receptor binding site that contributes to increased replication and virulence in mammals. In the present work, genetically very closely H9N2 viruses isolated from poultry and multiple non-poultry avian species. We demonstrated the existence of epidemiological links between poultry and other avian species kept in captivity. Therefore, these findings suggested the continuing surveillance of poultry and other avian species in this region. This demonstrates an epidemiological link between poultry and other avian species kept in captivity, a fact which must be considered in future H9N2 disease management programs.