Avian influenza is an infectious disease of birds caused by influenza type A virus belonging to the family Orthomyxoviridae. Long-term co-circulation of multiple virus lineages (e.g., H5N1 and H9N2 viruses) in different types of poultry has facilitated the frequent reassortment in H5N1 and H9N2 influenza viruses. This situation favors the emergence of influenza viruses with pandemic potential. Therefore it is important to know the detail molecular epidemiology of Bangladeshi LPAI H9N2 subtype. The objective of this study was the amplification and cloning of full length hemagglutinin gene of a low pathogenic H9N2 avian influenza virus. A full length hemagglutinin gene (1778 bp) of low pathogenic avian influenza was amplified by RT-PCR using HA (H9) gene specific primer. The amplicon was cloned in pGEM®-T Easy Vector (Promega, USA). The cloned cDNA was purified and sent to a commercial laboratory for sequencing. Phylogenetic analysis based on complete hemagglutinin (H9) gene sequence revealed that the Bangladeshi isolate of H9N2 LPAI is closely related to Indian isolates. Along with other isolates from South Asia and Middle East the Bangladeshi isolates belonged to A/Qauil/HK/G1/97(H9N2) like sub-lineage of H9N2 viruses.