K-casein (kappa-casein) is of special interest as a milk protein polymorphism due to its known relationship with milk quality and composition. A number of allelic variants have been identified in goats. In this study, genetic variants of the K-casein gene were evaluated in the South African Boer goat, Saanen and local unimproved goat types, using RFLP and DNA sequencing. The RFLP analysis revealed that the A/B allele group recorded the highest occurrence in all the goats studied. DNA sequencing confirmed the B allele (GenBank Acc. No. AF485340) to be the most common in all goat types, with allelic frequencies ranging from 0.593 in SA Boer goats to 1.0 in the Saanen. The B' allele (AY166706) was present
only in the SA Boer goat and local unimproved goat types with frequencies of 0.370 and
0.143, respectively. The Hallele (AF521022) was present at low frequencies in both the local
unimproved goat types (0.143) and the SA Boer goat (0.037), but absent in the Saanen goats.
AMOVA results indicated that most of the total variations occurred within populations (83.88%) with only 16.12% of the variation between populations. This study found limited genetic variation for K-casein to exist in the South African goat population.