South African (SA) indigenous and locally developed cattle breeds possess adaptive traits that are usually associated with tolerance to various diseases, extreme temperatures and humidity and to change in the availability of feed. These breeds are also adapted to low-input management system and have shown the ability to survive, produce and reproduce under harsh environments. Thus, these breeds hold potential in the changing South African production environments. However, little is still known about the nature or extent of the genetic variation underlying these breeds. Therefore, in this study, the Bovine SNP50 BeadChip was used to characterize the genetic diversity and population structure of SA cattle breeds, determine the level of linkage disequilibrium and conduct a genome wide scan for signatures of selection among the Afrikaner (n=44), Nguni (n=54), Drakensberger (n=47), and Bonsmara (n=46) using the Angus (n=31) and Holstein (n=29) cattle as reference groups since they have been characterized in other countries using similar tools. The first experiment performed included the evaluation of the Bovine SNP50 BeadChip to determine its utility for genome wide studies of South African cattle. Results of this experiment revealed that over 50 % of the SNPs were polymorphic (e.g. Nguni = 35 843), indicating that the Bovine SNP50 assay would be useful for genome wide studies among South African cattle breeds. The genetic diversity and population structure analyses indicated that the Afrikaner cattle had the lowest level of genetic diversity (He=0.24) while the Drakensberger cattle (He=0.30) had the highest among indigenous and locally-developed breeds. As expected, the average genetic distance was the greatest between indigenous breeds and Bos taurus breeds but the lowest among indigenous and locally-developed breeds. Model-based clustering revealed some level of admixture among indigenous and locally-developed breeds and supported the clustering of the breeds according to their history of origin. The analyses of the extent of linkage disequilibrium (LD) showed that Afrikaner, Angus and Holstein had higher LD compared to Nguni, Drakensberger and Bonsmara cattle at all tested genomic distances. The higher LD within the Afrikaner cattle suggested that this breed has experienced considerable selection forces in contrast to what is expected of indigenous breeds and would require lower marker (50 000) density relative to what will be required for the Nguni, Drakensberger (150 000) and Bonsmara (75 000) cattle for genome wide studies. Lastly, a genome wide scan for signatures of selection revealed a number of genes (KRT222, KRT24, KRT25, KRT26 and KRT27) and one heat shock protein (HSPB9) on chromosome (BTA) 19 at 41,447,971-41,926,734 bp in the Nguni that have been previously associated with adaptation to tropical environments in Zebu cattle. Furthermore, a number of genes associated with nervous system (WNT5B, FMOD, PRELP, ATP2B), immune response (CYM, CDC6, CDK10), production (MTPN, IGFBP4, TGFB1, AJAP1) and reproductive (ADIPOR2, OVOS2, RBBP8) performances were detected to be under selection in this study. The results presented on this thesis forms the basis for effective management of South African cattle breeds.