The H9 low-pathogenic avian influenza (LPAI) viruses cause enormous economic harm despite their low pathogenicity. It became common in Egypt in 2011 and has undergone ongoing genetic evolution since then. To limit the virus's transmission, regular monitoring of its evolution is essential. The current study concentrated on the frequency and molecular characteristics of LPAI H9N2 viruses spreading throughout different Egyptian areas between 2020 and 2022. Using real-time PCR, 503 positive LPAI H9 cases were detected out of 29,319 cases, for a total prevalence rate of 1.7%. However, live bird market (LBM) had the highest LPAI H9N2 prevalence rate (10.6%), followed by household sector and farm (2 % and 1.3% respectively). The 33 samples were isolated in 11-day-old embryonated chicken eggs (ECEs) before being sequenced for partial hemagglutinin (HA). The H9 isolates were phylogenetically related to the Egy-2 G1-B branch (pigeon-like), which has been the prevalent circulating H9N2 genotype in Egypt since 2016. The findings of the sequence analysis revealed a clear genetic evolution compared to the original virus (A/quail/Egypt/113413v/2011), which shared 93.2–95.4% and 94.7-97.1% homology at the nucleotide and amino acid levels, respectively. In comparison to the reference Egyptian strain, the molecular analysis found 12 alterations in amino acid residues with genetic stability in the major locations. The majority of examined strains had five glycosylation sites in HA. However, some strains had an extra sites at position 105, 145, 258. Comparable to A/quail/Hong Kong/G1/97, and all strains had the substitutions H191and L234 in the HA gene, indicating a predilection for binding to human-like receptors. Because of continues genetic development of H9 viruses reported in this work, frequent viral surveillance is required for better management.