Limited genotyping of msp1, msp2 and glurp in malaria patients from a localized area of Western Cambodia revealed considerable variation in msp2 alleles but well-conserved msp1 and glurp. Longitudinal genotyping of cases with recurrent malaria during seven days of anti-malarial treatment showed homogeneous genotype dynamics and did not alter the outcome classification compared to conventional genotyping at baseline and Df; however it did serve to illustrate some of the inherent complexities when interpreting the parasitological basis of recurrent disease. Here, ATAD1 is linked to malaria.