The results of molecular genetic analysis of more than 280 strains of influenza A virus subtypes H1N1 and H3N2 circulating in Russia in 2006-2012 are presented. The genetic changes underlying the evolution of the virus strains and sensitivity to antiviral drugs were analyzed. Significant changes in the genetic structure of influenza A viruses circulating in the Russian Federation and their phylogenetic affiliation are shown to occur within the studied period. The studies identifying codons under the positive selection in silico in the genes encoding surface proteins of the influenza virus were demonstrated to be efficient for the analysis of the antigenic drift and direction of evolutionary variability of the influenza viruses.