Alpha-s2 casein has a significant influence on protein content in goat milk, and the technological properties important for cheese processing. Specific alleles (A, B, C, E and F) of the alpha (α)s2-casein gene (CSN1S2) result in higher protein, casein and fat content, and improved coagulation properties, which are useful for improved cheese making. The aim of this study was to investigate the polymorphism and genetic variation of CSN1S2 in South African dairy goats, using DNA sequencing technology. Sixty dairy goats (20 Saanes, 20 British Alpine, and 20 Toggenburg) and 20 meat-type goats were sequenced with four primers to distinguish among the seven known alleles for αs2-casein. A total of four alleles (A, B, C and F) for CSN1S2 were observed among the dairy- and meat-type populations with ten genotypes across the populations. The A allele and the AA genotype were the most frequent across the populations, with the favourable AC genotype being the most frequent (0.300) in the Saanen population. Two unique genotypes were detected in the Toggenburg (BB and BF) and one in the meat-type goats (CF). The results indicate moderate genetic variation for αs2-casein in the South African goat populations (42.3–63.6%). Low positive FST values suggest limited inbreeding. This study confirmed the presence of favourable alleles in the South African goat populations, indicating room for genetic improvement using directional selection for favourable genotypes.