A molecular epidemiology study was conducted to determine the distribution of antimalarial drug resistance alleles among field isolates of Plasmodium falciparum. Samples were obtained during an epidemic affecting Kuna Amerindians in Panama. A high prevalence of mutations associated with chloroquine, pyrimethamine, and sulfadoxine was observed. Genotype analysis of msp2 revealed a low genetic diversity of P. falciparum parasites circulating in the studied area. The public health implications of these findings for the Central American region are discussed.