Abstract: Eight Newcastle disease virus (NDV) isolates from waterfowl such as geese and duck were obtained in China during 19962005, and then the fusion (F) protein gene and haemagglutinin-neuraminidase (HN) gene of those isolates were amplified and sequenced for further phylogenetic analysis. Phylogenetic trees were constructed separately based on variable region fragment (47420 nt) of the F gene and full-length deduced amino acid sequence of the HN gene of 40 NDV strains, including 16 NDV reference strains in the world and the 24 prevalent waterfowl NDV isolates. The results showed that 16 NDV reference strains were identical in the two different phylogenetic trees. While, only 15 in 24 NDV isolates from waterfowl were similar, the others were different. In addition, 24 waterfowl-derived NDV strains were all classified as genotype Ⅶ on the basis of deduced amino acid sequence of the HN gene, which were different from that by F gene. Furthermore, there had feeble correlation between the complete F and HN protein sequences, and highly close correlation between full-length F protein sequences and variable region fragments. The results showed that evolutionary rates of the F and HN genes were respectively independent. All those data showed that waterfowls might be the major reservoir hosts of NDV and we should pay more attention to those NDV strains isolated from waterfowls.