Although Ethiopia has an overall lower prevalence of Plasmodium falciparum among countries in Africa, the emergence of drug resistance could seriously hinder elimination efforts. Using samples collected from five therapeutic efficacy studies conducted in 2007-11, we evaluated the prevalence of putative drug resistance mutations in the pfcrt, pfmdr1, and kelch13 genes at the time of those studies, as well as the ama1 gene for genetic relatedness using a pooled amplicon deep sequencing approach. Among all sites, the kelch13 gene showed no mutations, whereas the pfcrt CVIET genotype was fixed in all populations. By contrast, the mdr1 gene demonstrated frequencies of resistant genotypes ranging from 10 to 100% at amino acid position 86 and from 0% to 57.8% at amino acid position 1246. Although we observed a low degree of haplotype sharing between sites, we did observe considerable haplotype sharing within sites over time. This suggests that P. falciparum populations in Ethiopia are isolated and able to persist through time.