Population genetic study of nine aboriginal ethnic groups of Taiwan (Ami, Atayal, Bunun, Paiwan, Puyuma, Rukai, Saisiat, Tsou, and Yami) was carried out. Twelve red cell enzymes (AcP, AK, CA1, CA2, EsD, GLO, GPT, GOT, LDH, MDH, PGD, and PGM1) were analyzed by isoelectric focusing method and starch gel electrophoretic method. Six loci (AcP, EsD, GLO, GPT, PGD, and PGM1) were polymorphic. Three alleles (PGM1*6, GPT*6, and EsD*7) were in relatively higher allele frequencies in Taiwan aboriginal populations, and we found homozygotes for those alleles. Phylogenetic relationship based on genetic distances among those ethnic groups more or less fit to their geographical distribution, but not to linguistic classification.