The genetic variations of the ten proteins in plasma and red cell were studied by the gel electrophoretic methods in Cheju native horse. Among the 10 proteins analysed in this study, 7 proteins (A1, Es, Pi, Hb, 6-PGD, PGM, Tf) were very polymorphic, while 3 proteins (Hp, MDH, ME) were monomorphic. The alleles showing the highest frequency in 7 proteins were A1B(0.602), Es1 (0.712), PiL(0.491), TfF(0.674), HbB1(0.620), 6-PgdF(0,823), PgmF(0.434), respectively.