Indian-origin Gir and Ongole cattle are international transboundary breeds that are reared in Brazil, The United States, Mexico, Malaysia, Panama, and other nations to provide meat and dairy products. These breeds have shown substantial genetic diversity in recent years and well suited to the ecological niche in Brazil. 90 cattle samples of Indian Gir (n = 15), Ongole (n = 17), Brazilian Gyr (n = 27), and Nellore (n = 31) breeds were genotyped using Illumina BovineHD BeadChip. Samples were analyzed to identify selection signature using two complementing approaches: Integrated Haplotype Score (iHS) and Fixation Index (FST). Gir versus Gyr and Ongole versus Nellore revealed Pairwise FST differences of 2.85 % and 2.35 %, respectively. Using integrated haplotype score (iHS) method, 4004, 3322, 3437, and 3485 genes were found in Gir, Gyr, Ongole, and Nellore, respectively, underlying top 1 % of selected regions. Under top 1 % of selected regions, FST based method identified1897 genes for the Ongole-Nellore pair and 1966 genes for the Gir-Gyr pair. Runs of homozygosity (ROH) analysis revealed that both recent as well as ancient inbreeding in these breeds were in range of 2.6-4.5 % indicating populations to be less inbred. Numerous candidate genes, including IER5, MILR1 (immunity related traits) in Gir; and FGF12, SV2C, JMY (average daily gain, body size, reproduction related traits) in Ongole, were found under the top-selected regions. Nellore breed had carcass/growth traits (PARP2, and KCNJ11) and genes linked to mammary gland development, udder size, and carcass (MYO16, MYO1B) were found in Gyr. Present findings reveals that Brazilian cattle population (Gyr and Nellore) is more selected for carcass and growth traits along with milk production traits, whereas in Indian cattle population (Gir and Ongole) selection signature related to immunity and adaptation were more prominent. Further, sufficient genetic diversity exist within these cattle breeds for their genetic improvement.