Background : Regular monitoring of the levels of anti-malarial resistance ofPlasmodium falciparumis an essentialpolicy to adapt therapy and improve malaria control. This monitoring can be facilitated by using molecular tools,which are easier to implement than the classical determination of the resistance phenotype. In Cameroon,chloroquine (CQ), previously the first-line therapy for uncomplicated malaria was officially withdrawn in 2002 andreplaced initially by amodiaquine (AQ) monotherapy. Then, artemisinin-based combination therapy (ACT), notablyartesunate-amodiaquine (AS-AQ) or artemether-lumefantrine (AL), was gradually introduced in 2004. This situationraised the question of the evolution ofP. falciparumresistance molecular markers in Yaoundé, a highly urbanizedCameroonian city. Methods : The genotype of pfcrt 72 and 76 andpfmdr186 alleles andpfmdr1copy number were determinedusing real-time PCR in 447P. falciparumsamples collected between 2005 and 2009. Results : This study showed a high prevalence of parasites with mutantpfcrt76 (83%) andpfmdr186 (93%)codons. On the contrary, no mutations in the pfcrt 72 codon and no samples with duplication of thepfmdr1genewere observed. Conclusion : The high prevalence of mutant pfcrt 76T andpfmdr186Y alleles might be due to the choice ofalternative drugs (AQ and AS-AQ) known to select such genotypes. Mutant pfcrt 72 codon was not detecteddespite the prolonged use of AQ either as monotherapy or combined with artesunate. The absence ofpfmdr1multicopies suggests that AL would still remain efficient. The limited use of mefloquine or the predominance ofmutantpfmdr186Y codon could explain the lack ofpfmdr1amplification. Indeed, this mutant codon is rarelyassociated with duplication ofpfmdr1gene. In Cameroon, the changes of therapeutic strategies and thesimultaneous use of several formulations of ACT or other anti-malarials that are not officially recommended resultin a complex selective pressure, rendering the prediction of the evolution ofP. falciparumresistance difficult. Thispublic health problem should lead to increased vigilance and regular monitoring