Influenza A virus has the ability to overcome immunity from previous infections through acquisition of genetic changes. Thus, understanding the evolution of the viruses in humans is important for surveillance and the selection of vaccine strains. A total of 30 influenza A/H3N2 viruses and 35 influenza A/H1N1 viruses that were collected in Vietnam from 2001 to 2006 were used to analyze the evolution of the HA, NA and M genes. Phylogenetic analysis of individual gene segments revealed that the HA and NA genes of the influenza A viruses evolved in a sequential way. However, the evolutionary pattern of the M gene proved to be nonlinear and was not linked with that of the HA and NA genes. Genetic drift in HA1 segments, especially in antigenic sites of A/H3N2 viruses, occurred more frequently when compared with A/H1N1 viruses. Two reassortants, one influenza A/H3N2 strain and one A/H1N1, were found based on the phylogenetic analysis of the three genes. While both genetic mutation and reassortment contributed to their evolution, the frequency of genetic changes and reassortment events differs between the two subtypes. As influenza circulate throughout the year, we emphasize the importance of surveillance in tropical and subtropical zones, where emergence of new strains may be detected earlier than in temperate zones.