Seventy five plasma samples of Cheju native horse were analysed by a simple method of two-dimensional(2-D) agarose gel(pH8.6)-horizontal polyacrylamide gel(pH 9.0) electrophoresis, and the gels were stained with Comassie Brilliant Blue G 250. The fraction of albumin(AI). vitamin D binding protein(Gc), α1-protease inhibitor 1 and 2(Pi-1, 2), estcrase(Es), antithmmbinIII(AT3), haptoglobin (Hp), cojugation of Hp and hemoglobin(Hp-Hb), hemopexin(Hx), immunoglobulin G(Ig G). transterrin(Tf), and α1 B-giycoprotein(α1B) were identified by comparing wish the previous reports of Juneja et al.(1984, 1989). Three Gc phenotypes FF, FS and SS were observed, and their gene frequencies were calculated to be 0.42 for GcF and 0.58 for GcS, respectively. Three phenotypes of Cp observed were FF, FS and SS, and their gene frequencies were 0.34 for Cp^F and Up^S, respectively These two proteins were polymorphic, and controlled by two codominant alleles at an autosomat locus. The gene frequencies of allefes Gc^S and Cp^S in Cheju native horse populatictrt were higher than other horse breed populations. Therefore the 2-D electrophoresis system was very useful individual identification and parentage control in horse population.