Yellow, brindle and black Korean native cattle (Hanwoo) breeds have been raised in Korea, among which the yellow Hanwoo has been commercially selected for the needs of Korean beef consumers, while the breeding of the latter two breeds have been focused on mush less. Three sets of samples were collected randomly, i.e., 250, 18 and 18 individuals for the respective breeds, and genotyped with the 648K Affymetrix Axiom arrays. After quality control tests (MAP > 0.05, H-W > 0.0001, call rate > 0.9)), the numbers of available SNPs were 401K (62%), 343K (53%), and 328K (51%), with average distances (stsndard deviation) between aduacent SNPs 7.0 (9.7), 8.2 (11.8), and 8.6 (12.3) kbp, respectively. Among the available SNPs, 1143, 2518 and 16,155 SNPs were found with allele frequency difference ( > 0.5) between yellow-brindle, yellow-black and brindle-blasck Hanwoo breeds, respectively. Also, Linkage disequilibria (LD) were measured using r2 values (GOLD program). The average values were 0.28, 0.37 and 0.40 between SNPs within 1 kbp, and 0.21, 0.31 and 0.34 within 1-10kbp distance for the greatest LD for the black Hanwoos, indicating the greatest LD for the black and smallest LD for the yellow Hanwoo breeds. A set of 287 SNPs with great allele frequency differences between the three breeds were selected to test breed indentification, for which Structure program (v 2.3.4) was applied such that 97%, 86% of the yellow, brindle and black Hanwoo individuals were correctly indentified as their respective Korean native breeds.