In recent years there has been a considerable debate on the population genetic structure of malaria parasites. Work on this subject has been revolutionized by the advent of the polymerase chain reaction (PCR) technique, which has made it feasible to study the genetic diversity of parasites in small samples of infected blood, allowing extensive surveys of natural parasite populations to be made. In addition, the technique can be applied to the mosquito stages of the malaria parasite, allowing direct assessments to be trade of the frequency of crossing between parasite clones in Nature. Studies on Plasmodium falcjparum in a wide range of malaria-endemic regions are now revealing the relationship between parasite population structure and malaria epidemiology. In this article, Hamza Babiker and David Walliker review recent work in this field, and discuss how such knowledge might be used to advise on the future deployment of control measures such as antimalarial drugs and possible malaria vaccines.