Jeju Black cattle is one of the aboriginal Korean cattle breeds that has been isolated in Jeju island for a long time, while Yellow Hanwoo cattle has been extensively selected for beef production traits for the last several decades. Aiming to investigate broader patterns of selection, we genotyped 352 Yellow Hanwoo and 169 Jeju Black cattle using a customized 150 K bovine chip. Our composite selection signals’ analysis to identify selection signatures (cross-population extended haplotype homozygosity [XP-EHH], ΔSAF, and FST) identified recent and strong signature of selection near many loci with mutations affecting the traits under strong selection as outlier in Yellow Hanwoo, including SCP2 (P = 8.41 × 10−10) that may be involved in the meat quality. We found nine candidate regions with significant clusters of selection signals.