The evolutionary selection of malaria parasites within an individual host plays a critical role in the emergence of drug resistance. We have compared the selection of atovaquone resistance mutants in mouse models reflecting two different causes of failure of malaria treatment, an inadequate subtherapeutic dose and an incomplete therapeutic dose. The two models are based on cycles of insufficient treatment of Plasmodium berghei-infected mice: repeated inadequate treatment associated with a subtherapeutic dose (RIaT) (0.1 mg kg Ϫ1 of body weight) and repeated incomplete treatment with a therapeutic dose (RIcT) (14.4 mg kg Ϫ1 of body weight). The number of treatment cycles for the development of a stable resistance phenotype during RIaT was 2.00 Ϯ 0.00 cycles (n ϭ 9), which is not statistically different from that during RIcT (2.57 Ϯ 0.85 cycles; combined n ϭ 14; P ϭ 0.0591). All mutations underlying atovaquone resistance selected by RIaT (M133I, T142N, and L144S) were found to be in the Qo1 (quinone binding 1) domain of the mitochondrial cytochrome b gene, in contrast to those selected by RIcT (Y268N/C, L271V, K272R, and V284F) in the Qo2 domain or its neighboring sixth transmembrane region. Exposure of mixed populations of resistant parasites from RIaT to the higher therapeutic dose of RIcT revealed further insights into the dynamics of within-host selection of resistance to antimalarial drugs. These results suggest that both inadequate subtherapeutic doses and incomplete therapeutic doses in malaria treatment pose similar threats to the emergence of drug resistance. RIcT and RIaT could be developed as useful tools to predict the potential emergence of resistance to newly introduced and less-understood antimalarials.KEYWORDS dose-dependent selection, mouse malaria model, repeated inadequate treatment, repeated incomplete treatment, within-host selection of atovaquone resistance T he evolutionary selection of malaria parasites within an individual host plays a critical role in the emergence of antimalarial drug resistance, a major problem in malaria control. The study of within-host selection of drug resistance benefits from animal models of malaria infection, as it allows pharmacological manipulations in vivo.We recently reported such a model, based on cycles of repeated incomplete treatment (RIcT) of Plasmodium berghei-infected mice with a constant therapeutic dose of an antimalarial drug, which mimics treatment failure in the human field situation (1). We showed that under these conditions, stable resistance of P. berghei to the antimalarial atovaquone developed rapidly, after only 2.5 cycles of treatment.