Numerous studies have explored the molecular epidemiology of H9N2 viruses in Iran; however, continuous monitoring remains vital for timely interventions to mitigate potential damage. This study examined the molecular characteristics and evolutionary features of Iranian H9N2 viruses by sequencing the complete genomes of two viruses, Marand and Baneh, isolated in 1998 and 2022, respectively, alongside other Iranian strains from GenBank. All Iranian viruses were identified as low-pathogenic avian influenza viruses, as evidenced by the presence of the di-basic motif K/RSSR cleavage site. Notably, all Iranian viruses isolated from 2009 onward had an L at position 216 in the hemagglutinin receptor binding site, whereas earlier viruses exhibited a Q/L at the same position, an essential mutation that enhances replication in mammalian cells. The molecular evolutionary rates for the Iranian hemagglutinin (HA) and neuraminidase (NA) genes were estimated at 4.50 × 10^-3 and 3.60 × 10^-3 substitutions per site per year, respectively. Error-prone replication of H9N2 viruses has resulted in the continuous evolution of Iranian strains over two decades, characterized by three phases of population growth. Maximum likelihood phylogenetic analysis revealed that the HA and NA genes of H9N2 viruses from domestic chickens belonged to the G1 sublineage. Additionally, the internal genes of some viruses displayed evidence of reassortment with other subtypes, indicating potential gene exchange with other viruses. These findings underscored the importance of ongoing surveillance of H9N2 viruses in both domestic and wild bird populations, given the human-like receptor-binding preference and the possibility of genetic reassortment with various viral subtypes.