The goals of this study was to: (1) compare the results of HRM to those using PCR–RFLP in the context of drug resistance marker surveillance in a malaria endemic country; and, (2) to determine the prevalence of mutations N51I, C59R, S108N in the dhfr gene and A437G, K540E, A581G, A613T/S in the dhps gene, across two malaria endemic settings with distinct frequencies of polyclonal infections (infections harbouring more than 1 parasite genome), as determined by MSP 1 and 2 genotyping. This evidence concerns the gene DHPS and malaria.