Detection of selection signals using genomic data is vital for tracking drug resistance loci in microorganisms that cause disease, such as malaria, and monitoring of such loci is crucial for disease control efforts. Here we present a novel method of detecting relatively recent selection using identity-by-descent approaches suitable for multiclonal, recombining microorganisms. Application of this new method to a large whole genome sequencing study of Plasmodium falciparum identifies many well-known signatures such as crt and k13, associated with chloroquine resistance and artemisinin resistance respectively, and through relatedness networks shows how these signatures are distributed in Southeast Asia, Africa and Oceania. Using these networks, we confirmed an independent origin of chloroquine resistance in Papua New Guinea and the spread of multiple artemisinin resistance mutations in Southeast Asia. We also found two novel signals of selection not yet investigated in detail.