The main objective of this investigation was whether the combination therapy of sulfadoxine pyrimethamine (SP) plus artesunate (AS) protects against the spread of resistance to SP in malaria-endemic south-eastern Iran. Infected blood samples of Plasmodium falciparum (n=170) were collected during 2008-2010 after the adoption of SP-AS as the first line treatment in Iran. Four different genes of P. falciparum [dihydropteroate synthetase (pfdhps), dihydrofolate reductase (pfdhfr), chloroquine (CQ) resistance transporter (pfcrt K76T) and multidrug resistance1 (pfmdr1 N86Y)], associated with SP and CQ resistance were analyzed using PCR-RFLP methods. The result showed 4.1, 95.9 and 100% prevalence of pfdhfr 51I, 59R and 108N, respectively and the majority of patients (95.9%) were found to carry both 59R and 108N. The prevalence of single mutation at pfdhps 437G gene was 26.9% before the adoption of SP-AS, but as SP was used as the first line treatment; this mutation started to increase and reached a high level of 55.5% in 2008 (χ(2) test, P<0.05). However, three years after the introduction of SP-AS, this prevalence was reduced from 55.5% (in 2008) to 39.1% (in 2009) and then 40.5% (in 2010). The frequency of parasites carrying pfdhfr/pfdhps mutations (N(51)R(59)N(108)/G(437)) decreased from 53.3% in 2008 to 39.1% in 2009 and 38% in 2010. In addition, no significant reduction was seen in the frequency of mutant alleles of pfcrt 76T and pfmdr1 86Y after CQ was discontinued from study areas as a treatment for P. falciparum. This is explained by the fixation of pfcrt 76T in the falciparum populations that need more time to recover from CQ sensitivity in the absence of drug pressure in this region. In conclusion, the present findings suggest that in Iran, SP is still effective for the treatment of uncomplicated falciparum malaria as a partner drug of Artemisinin Combination Therapy (ACT) in this region.