Afrikaner, Drakensberger, and Nguni are the South African (SA) landraces that played major roles in the social, cultural and economic history of SA. These breeds are valuable genetic resources for beef production and limited information is available for these breeds at the genome level. The aim of this study was to perform SNP discovery in these three breeds using whole genome sequencing. Ninety cattle representing the three breeds were used to identify more about 17.6 M putative variants including SNPs and Indels. DNA was extracted from blood and hair samples, quantified and prepared at 50ng/?l concentration for sequencing at the Agricultural Research Council Biotechnology Platform using an Illumina HiSeq 2000. The fastq files were used to call the variants using the Genome Analysis Tool Kit. A total of 4,369,879 (16% of the total SNPs) were identified as novel. Annotation of these variants classified them into functional categories. Within the coding regions, 43% of the SNPs were nonsynonymous substitutions that encode for alternate amino acids. Functional enrichment analysis of novel SNPs identified significant number of genes (p < 0.001) that were located within 5% of 1,481 100kb windows. Gene ontology terms identified genes such as MLANA and SYT10 that have been associated with coat colour and sense of smell in mouse, respectively, and the ADAMS3 gene has been associated with fertility in cattle. Furthermore, whole genome screening detected 688 candidate selective sweeps (ZHp Z-scores ? -4) across all three breeds, of which 223 regions were assigned as being putative selective sweeps (ZHp scores ? -5). We also identified 96 regions with extremely low ZHp Z-scores (? -6) in Afrikaner and Nguni. Several genes such as KIT and MITF that have been associated with skin pigmentation in cattle, and CACNA1C, which has been associated biopolar disorder in human were identified in these regions. Breed-specific SNPs (2,272,667) were identified across the breeds and only 186 of these SNPs were identified as putative breed-specific SNPs. These SNPs were further tested for their ability to assign individuals to a breed and need further validation. This study provides the first analysis of sequence data to discover SNPs in indigenous SA cattle breeds. These results provide insight into the genetic composition of the breeds and offer the potential for further applications in their genetic improvement.