Genetic markers were examined on a total of 1,027 blood samples collected from the Aeta of Luzon and the Mamanwa of Mindanao as well as 4 other Negrito groups of the Philippines. Genetic distance analyses by means of Nei's method were carried out using frequency data for up to 21 polymorphic loci. The geographical distributions of protein variants showing private polymorphism were also examined. It was shown that (1) the Negrito populations examined, except the Mamanwa, form one cluster group on the dendrogram, (2) no close relationship exists between the Negritos and Africans, (3) Negritos are more closely related to south-east Asian populations than to Australian Aborigines and New Guineans. It is postulated that the Mamanwa are derived from the ancestral Proto-Malay population of late-Pleistocene Sundaland, from which the Negritos also evolved with a phenotypic specialization of small body size probably due to the adaptation to tropical rain forest.