Sulfadoxine-pyrimethamine (SP) resistance in Plasmodium falciparum is encoded by a number of mutations in the dihydrofolate reductase (dhfr) and dihydropteroate synthetase (dhps) genes. Here, we have characterized point mutations in dhfr and dhps and microsatellite loci around dhfr on chromosome 4 and dhps on chromosome 8 as well as neutral markers on chromosomes 2 and 3 in 332 samples from Yaoundé, Cameroon. The triple mutant dhfr haplotype that originated in Southeast Asia is the most predominant in this sample set, but we also find additional independent haplotypes at low frequency and an incipient process of genetic differentiation among alleles of Southeast Asian origin. As reported for other African populations, we find evidence of a selective sweep for resistant dhfr mutants in this Cameroonian population due to drug selection. Although we find evidence for a selective sweep in dhps mutants associated with SP resistance, the dynamics of dhps mutants appear different than those observed for dhfr mutants. Overall, our results yield support for the use of microsatellite markers to track resistant parasites; however, the detection of resistant dhfr alleles in low frequency, the evidence of divergence among dhfr alleles that share a common evolutionary origin, and the distinct dynamics of resistant dhps alleles emphasize the importance of comprehensive, population-based investigations to evaluate the effects of drug selection on parasite populations.Plasmodium falciparum resistance to the most commonly used antimalarial drugs has been detected worldwide, reaching the level of a public health emergency (15, 37). Resistance to chloroquine has led to the discontinued use of the drug in many parts of the world, and resistance to sulfadoxine-pyrimethamine (SP), an affordable and widely available alternative to chloroquine, has rendered this drug ineffective in many areas as well.Malaria control programs around the world are turning to artemisinin-based combination therapies. However, policy decisions to delay the emergence of resistance against artemisinin-based combination therapies must be made before critical information is widely available. Thus, the fundamental understanding of how resistance against drugs such as SP and chloroquine emerges and how this resistance disseminates will provide critical information for developing strategies to identify and contain resistance to other drugs. In addition, because of its safety for pregnant women and infants and its long action, SP is the only drug recommended for intermittent preventive treatment in these vulnerable populations, and new antifolate combinations are under development (15). Thus, understanding the dynamics of mutations associated with resistance against SP is still a matter of great epidemiologic and public health importance.SP acts as an inhibitor of the P. falciparum folic acid pathway, and point mutations in the genes encoding dihydrofolate reductase (DHFR) and dihydropteroate synthetase (DHPS) have been implicated in SP resistance (16). Point mutati...