This study set objectives to assess current practical efficacy of coartem and to estimaternfrequency of resistance molecular markers to chloroquine/fansidar in pfdhfr, pfcrtK76T, andrnpfmdrN86Y alleles. Therefore, an in vivo therapeutic efficacy study for 14 days of follow-uprnwas conducted in Humera from September-December, 2006. Moreover, field isolates wererngenotyped by RT-PCR. rnrnOne hundred and eighteen patients aged 2 to 65 years with microscopicly confirmedrnPlasmodium falciparum, were recruited. On enrollment, the mean parasite density was 21,488rn/Âµl and all had documented history of fever. In addition, about 4 drops of blood was blotted onrn3 MM Whatman filter paper for genotyping. All were treated by coartem twice a day for threerndays, with16 patients lost to follow-up. The remaining 102 volunteers completed follow-uprnsuccessfully with 100% adequate clinical and parasitological treatment response to coartem.rnComplete fever and parasitaemia clearance was achieved within 2 and 3 days respectively in allrnpatients. Moreover, association between initial parasitaemia and parasitaemia clearance timernwas statistically significant (p-value=0.011) to effect clearance.rnrnThe frequency of field isolates carried triple mutant alleles was 12% in pfdhfr gen whichrndetermine a decline of high treatment response to SP in in vivo and in vitro susceptibility,rnparticularly pyrimethamine. The prevalence of individual mutations in pfdhfr51I, pfdhfr59R,rnand pfdhfr108N alleles was 78%, 17%, and 91.7% respectively. No mutation was observed in rnpfdhfr108 with amino acid substitution from Serine to Theronine. Frequency of pfcrt76T andrnpfmdr86Y mutation was 74.3% and 69.7% respectively with 51.4% mutation in both pfcrt76Trnand pfmdr86 Y alleles that are associated or implicated to determine resistance to chloroquine. rnrnMoreover, field isolates carrying mutant allele pfdhfr51I tend to cause infection in younger agern(p-value=0.028). Parasitaemia clearance time was prolonged in patients infected by fieldrnisolates carried a mutant allele of pfcrt76T (p-value=0.0001) and pfmdr86Y (p-value=0.011).rnAssociation was strong in field isolates carrying both pfcrt76T and pfmdr86Y (p-value=0.0001) in comparison to an individual alleles. No association was found between genotype and age inrnall age groups. rnrnBased on the present results, it was concluded that in Humera Ethiopia AL therapeutic efficacyrnis high to treat uncomplicated P. falciparum malaria and effective against chloroquine andrnfansidar resistant parasites where a high prevalence of pfdhfr, pfcrt76T, and pfmdr86Yrnmutations was observed. Therefore, for a better understanding, further studies should bernconducted in a multi-center fashion representing epidemiology over all of Ethiopia.