Abstract: An H4N6 subtype avain influenza virus(AIV), A/mallard/Yancheng/2005（H4N6）,was isolated from cloacal swab of mallard in the national protection grade in Yancheng country. The eight full-length genes， including the 5′and 3′ends of virus were amplified by using the universal primers. Amino acid sequence comparisons and phylogenetic analysis of A/mallard/Yancheng/2005（H4N6）AIV was made with other sequences available in the Influenza Sequence Database. The results showed that the motif of HA cleavage site is PEKASR， which was the characteristics of low pathogenic AIV. Both the NA and NS gene had no residue lost. The amino acid residues related to host specialty of matrix protein 2 were all avain specialty，and the 627 residue of PB2 was Glutamic acid (E). The nucleotide homology of M gene with A/duck/Yangzhou/02/2005(H8N4) AIV was 99.4%, the PA gene had genetically close relationships with that of A/duck/Jiangxi/1286/2005(H5N2) AIV, these results suggest that both M and PA gene had circulated in the domestic duck and involved in gene reassortment.