Until quite recently, very little information has been available about the genome content and structure of parasitic protozoa. This inadequacy has been rectified by the advent of high-throughput strategies that permit sequencing of whole genomes and enhanced computational capacities that render this information tractable. The current list of complete or near-complete genomes includes some of the greatest scourges of humans and their domesticated companions. Among these miscreants are several members of the genus Plasmodium, the agents of malaria. Scores of species of Plasmodium have been described and comprise pathogens of every major group of terrestrial vertebrates. At present, no less than seven of these species are subjects of major genome-sequencing projects, and it is anticipated that the comparison of these genomes will provide invaluable insights as to how genomic contents may mediate the interaction of the parasite with its host (1). Our understanding of genome structure and function has been facilitated by models of evolutionary biology, and these findings validate theoretical predictions about genome evolution that predate by several decades our ability to collate their contents (2). Coupled with these comparative approaches to understand how genomes have shaped different species are studies that use the new information about genome polymorphism to better under understand the population structure and evolutionary history of individual species. The article by Leclerc et al. (3) in a recent issue of PNAS exemplifies how “population genomics” provides a means of examining the evolutionary forces acting, in both the past and present, on a species. The authors assayed polymorphism at several genetic loci of the human malaria parasite, Plasmodium vivax, and compared the extent of this polymorphism with that of other closely related primate malaria species. Like previous reports of a paucity of genetic polymorphism in the malignant malaria parasite Plasmodium falciparum (4, 5), Leclerc et al. (3) found extremely low levels of polymorphism in P. vivax and concluded that a selective sweep and/or population bottleneck must have occurred in this species' recent evolutionary past.