Objective:To analyze evolutionary characteristics of the matrix protein (M) and nucleoprotein (NP) genes of influenza virus A/H1N1 in 2009 pandemic.Methods: The M and NP genes of A/H1N1 viruses were downloaded from NCBI database.MEGA4.0 software and NJ method were used for sequence alignment,protein sequence alignment,and the phylogenetic tree construction.Meanwhile,Epi Info software was used to analyze the linear trend of evolutionary distance of the M and NP genes of human H1N1 strains isolated during 1918 to 2009.Results: The M and NP gene sequences were similar among the novel A/H1N1 viruses,but different from those of the previous influenza H1N1 viruses.Using reference sequences of human H1N1 strains isolated during 1918 to 2008,we found that changes in evolutionary distances of the M genes between novel A/H1N1 strains and each of the reference A/H1N1 strains increased with increasing year intervals (Ptrend = 0.001).Compared with the amino acid sequence of M2 protein of reference human A/H1N1 virus strains isolated during 1918 to 2008,the novel A/H1N1 viruses had the amino acid substitutions at 6 sites: 11,43,54,57,77,and 78.Compared with swine and avian A/H1N1,the novel A/H1N1 virus only had the amino acid substitutions at 43 and 77.Conclusion: The NP gene of novel A/H1N1 virus,which is routinely considered as a conserved sequence,is different from those of the previously isolated human H1N1 influenza viruses; the related mechanisms and consequences on viral activity remain to be elucidated.The substitution to threonine at 11 and 43 amino acids of M2 protein might contribute to amantadine resistance of the novel H1N1 virus pandemic in 2009.