We have compared allelic polymorphism of two merozoite surface protein genes, MSP-1 and MSP-2, of Plasmodium falciparum and the parasite load in infected individuals in two villages in east Africa. In Michenga village in Tanzania, malaria is holoendemic and transmission is perennial; in Asar village in Sudan, malaria is mesoendemic and transmission is markedly seasonal. The numbers of alleles of both genes were found to be much greater in Michenga than in Asar. More parasite clones exhibiting higher allelic polymorphisms of the genes studied were carried by infected inhabitants in Michenga than those in Asar. The high mean number of clones in Michenga is associated with a very high frequency of out-crossing compared with that estimated in Asar.