Abstract: In order to explore the genetic mutations of the hemagglutinin gene and the neuraminidase gene and the law of molecular epidemiology of H9 subtype avian influenza in China, ten avian influenza virus subtype H9N2 were isolated from some poultry yards in Northern China, the whole HA and NA cDNA fragments of them were amplified by reverse transcription polymerase chain reaction, with primers specific to HA gene and NA gene. After cloning and sequencing, gene sequences were analyzed on homology and heredity evolution. The sequence analysis showed little degree of variation, the various types and the high rate of mutation. They belonged to a branch of the CBJ194-like in the phylogenetic tree. The nucleotide homology of the HA gene to the CBJ194 was from 88.8% to 95.8%. The nucleotide homology of the NA gene to the CBJ194 was from 93.4% to 97.6%, so they might come from the same ancestor AIV strain. Because of the gene mutation, the new potential glycosylation site appear in the HA gene of the ACHB101 and a stenoplastic receptor-binding site have changed in ACHN102. In the deduced amino acids sequence, the 63, 64 and 65 sites lost T, E and I, which cause loss of the 61 glycosylation sites. Otherwise, there was conspicuous mutation in the acetylneuraminic acid adsorption sites. These findings may be fruitful for making further study of genetic mutations of AIV in the field and improving the control strategies.