Abstract: In order to explore the genetic mutations of the neuraminidase and the law of the molecular epidemiology of H9N2 subtype Avian Influenza virus (AIV) in mainland of China, 63 H9N2 AIV strains were isolated from some poultry yards in China, the whole NA cDNA fragments of them were amplified by reverse transcription polymerase chain reaction, with primers specific to NA gene. After cloning and sequencing, homology and heredity evolution of NA gene sequences were analyzed. The sequence analysis showed that the homology of NA gene in this study was between 87.4%-99.5% Neuraminidase of 52 strains had a deletion of 3 amino acid residues at positions 63-65, belong to Y280-like branch; the other 11 strains had no deletion in the stalk, belong to G9like branch. Amino acid residues at hemadsorbing (HB) sites and antigenic determinants of these isolates exist variation. The amino acid residues in the enzyme active sites of the isolates were highly conserved and showed no mutations associated with resistance to the sialidase inhibitors oseltamivir and zanamivir. 36 strains viruses sequenced in this study contained potential glycosylation sites at 264 amino acid residues 28 strains lost potential glycosylation sites at 402 amino acid residues. The results indicated that by now the NA gene of H9N2 AIV in mainland China belong to two branches, Y280-like and G9-like, and the most NA gene of the H9N2 isolates in China mainland belong to Y280-like.