The World Health Organization (WHO) recommends that parasitological confirmation of clinical malaria diagnosis be performed before antimalarial treatment is administered. Malaria rapid diagnostic tests (RDTs) represent a valuable tool for prompt and efficient diagnosis of malaria in settings where microscopic diagnosis is unavailable or unreliable. Concerns remain, however, that Plasmodium falciparum polymorphisms in the genes coding the antigens detected by RDT could impact on RDT performance. Using field isolates of Plasmodium falciparum, we aimed to characterize genetic variability in histidine-rich proteins 2 and 3 (PfHRP-2 and PfHRP-3), aldolase (ALD) and Plasmodium lactate dehydrogenase (pLDH) genes and to evaluate their impact on the performance of RDT. Pfhrp-2, Pfhrp-3, aldolase and pldh were amplified using polymerase chain reaction (PCR) and sequenced. Genetic variation was observed in pfhrp-2 and pfhrp-3 genes while aldolase and pldh showed high levels of conservation. These findings suggest that RDTs based on pLDH and ALD are reliable in the study settings where there is intense diversity or polymorphisms of histidine-rich protein (HRP). Nevertheless, there is no evidence from this study to suggest that RDTs based on the detection of PfHRP-2 and PfHRP-3 have lower sensitivity in Papua New Guinea (PNG). The results observed in this study will be used to inform the PNG National Department of Health on the continued usage of pLDH/ HRP-2 RDT for malaria diagnosis in PNG.