The frequency of the amantadine-resistant H1N1 influenza A virus has been increasing since the 2005-2006 season. It is unclear whether reassortment was involved in this trend. Here, we show that cocirculation of amantadine-resistant and -sensitive strains led to the genesis of amantadine-sensitive reassortant virus during the 2007-2008 season. Thereafter, the reassortant virus predominated. This contrasts with the trend for the H3N2 virus, in which the amantadine-resistant reassortant virus became predominant. The results suggest that it is necessary to monitor genome dynamics to understand the evolution and mechanism of the emergence and spread of antiviral resistance among influenza A viruses.