In order to clarify the genetic composition and to find possible genetic markers of Cheju native horses, the genetic variations of the nine proteins (Al, Pi, Es, Hp, Hb, PGD, PGM, MDH, ME) were investigated by the gel electrophoretic techniques. Al: There were two alleles, AlA and AlB. The alleles frequencies of AlA and AlB were 0.398 and 0.602, respectively(X2=0.02, d.f. = 2, P>0.9). Pi: Seven Pi alleles (PiF, PiG,, PiI, PiL, PiN ,PiS, and PiU) were detected. The gene frequencies of Pi were PiF 0.136, PiG, 0.496, PiI 0.260, and others( PiL, PiN ,PiS, PiU) 0.108, respectively(X2=62.48, d.f.=12, P<0.005). Es: there were three alleles, EsF, EsI,and EsS. The gene frequencies of Es were EsF 0.266, EsI 0.712 and EsS 0.022, respectively( X2=21.28, d.f.=3, P<0.005). Hb: Three alleles (HbA, HbBI, HbBII) were found. The gene frequencies of Hb were HbA 0.120, HbBI 0.620, HbBII 0.260, respectively (X2=2.63, d.f. =n 3, P>0.25). PGM: There were two alleles, PgmF and PgmS. The gene frequencies of PGM were PgmF 0.434 and PgmS 0.566, respectively(X2=0.22, d.f.=2, P>0.75). PGD: There were two alleles, PgdF and PgdS. The gene frequencies of PGD were PgdF 0.823 and PgdS 0.177, respectively(X2=7.53, d.f.=2, P<0.05). Three proteins(Hp,MDH,ME) showed the monomorphic traits in this population. the mean heterozygosity of nine protein loci were calculated as 0.329±0.012.