Amantadine and oseltamivir are used to treat influenza A virus infections; however, resistance to these drugs has been widely reported throughout the world. In this study, the frequency and genetic characteristics of the drug-resistant influenza A viruses that circulated in Thailand from 2006 to 2008 were investigated. The nucleotide sequences of the NA and M2 genes were elucidated in order to identify mutations that confer oseltamivir- and amantadine-resistant phenotypes, respectively. A total of 66 influenza A viruses including 44 H1N1 and 22 H3N2 subtypes isolated in Bangkok and 13 provinces of Thailand from 2006 to 2008 were analyzed. Our results demonstrated that seven out of 32 (22%) of the H1N1 viruses isolated in 2006 in Thailand carried the amino acid S31N substitution, which confers amantadine-resistance, although no isolates in 2007 or 2008 possessed the mutation. In the cases of oseltamivir-resistance, four of 10 (40%) of the H1N1 viruses isolated in 2008 were predicted to be resistant to the drug, although none of the 34 viruses isolated in 2006 or 2007 were predicted to be resistant. Surprisingly, all 9 H3N2 viruses isolated in 2008 appeared to be resistant to the amantadine and none were resistant in 2006 or 2007. Phylogenetic analysis based on the HA, M, and NA genes demonstrated that the amantadine-resistant H1N1 isolates had been produced by genetic reassortment. All of the amantadine-resistant H3N2 viruses were clustered in one of these three genes and possessed double mutations of S193F and D225N in the HA gene.