The aim of this study was to provide the first comprehensive spatiotemporal picture of Plasmodium falciparum resistance in various geographic areas in Madagascar. Additional data about the antimalarial resistance in the neighboring islands of the Comoros archipelago were also collected. We assessed the prevalence of pfcrt, pfmdr-1, pfdhfr, and pfdhps mutations and the pfmdr-1 gene copy number in 1,596 P. falciparum isolates collected in 26 health centers ( In recent decades, the emergence and subsequent spread of Plasmodium falciparum chloroquine (CQ)-and sulfadoxinepyrimethamine (SP)-resistant parasites across areas where malaria is endemic have been a challenge to malaria control programs (41, 44). Substantial advances toward gaining an understanding of the genetic basis of antimalarial drug resistance have been made (14). Molecular evolutionary studies have concluded that the CQ-resistant P. falciparum chloroquine resistance transporter (pfcrt) and high-level pyrimethamine-resistant dihydrofolate (pfdhfr) alleles have emerged in a limited number of independent foci, from which they have rapidly spread in the local vicinity and have then invaded areas continent-wide and transferred between continents (1, 36). These lessons of the past have, first, stimulated changes in antimalarial treatment policies by introducing combinations of drugs that act on different targets and, second, resulted in the implementation of effective monitoring systems to detect as early as possible the emergence of resistant parasites on the basis of the assessment of the therapeutic efficacies of antimalarials (25, 46), determination of the decreased sensitivity of the parasites to drugs in vitro (4), and the detection of an increasing prevalence of molecular markers related to drug resistance (24).According to data published from 2002 to 2006, the epidemiological features of P. falciparum CQ and SP resistance differ considerably between Madagascar and the Comoros Islands, two countries located close to each other in the southwestern Indian Ocean (43). In vitro CQ resistance was moderate in Madagascar (29,33,45), although the level of therapeutic efficacy was declining. During that time, the rate of CQ resistance was high in the Comoros Islands (22,23,30). Likewise, pyrimethamine resistance was absent in Madagascar (28, 32) but was present at high levels in the Comoros Islands (23). The most recent in vivo data obtained on the basis of the WHO 28-day follow-up protocol, conducted in 2006 and 2007 at multiple sites, have confirmed that resistance to all antimalarials except CQ in Madagascar remains rare. Indeed, the prevalence of the clinical failure of treatment with amodiaquine, SP and the combination artesunate and amodiaquine was Ͻ5%, while the rate of failure of treatment with CQ was 44% (19). However, the recent demonstration of the introduction of multidrug-resistant P. falciparum parasites into Madagascar from the Comoros Islands (18) and the emergence of the uncommon dihydrofolate reductase I164L genotype in P. falciparum parasi...