DNA sequence data reveal extensive polymorphism in the virulent, human malaria parasite Plasmodium falciparum. The extent of polymorphism at apparently neutral-evolving loci points to a common ancestor for this species that is no more recent than approximately 150,000-200,000 years ago. In addition, there is evidence of balanced polymorphisms at certain antigen-encoding loci, some of which have been maintained for millions of years. Thus, we can reject the hypothesis that this species underwent a recent extreme bottleneck (i.e. one in which the population was reduced to a single haploid genotype). However, it is possible that less-severe bottlenecks have occurred.