This study aims to use genome-wide sequencing to establish the structure of Plasmodium populations in an endemic area of low malaria transmission with occasional outbreaks, in the Pacific region of Colombia, and analyse the emergence, dissemination, and frequency changes of antimalarial drug resistance genotypes, the connectivity between parasite populations, and the way epidemiologic and demographic variables affect some of the parasite's genetic properties. Patterns of malaria transmission and parasite molecular information allow to characterize spatial malaria transmission units to inform malaria control programmes.