Genetic mutation occurs within genes and is responsible for the observed phenotypic variation between breeds within a species. It is known that indigenous sheep breeds are more robust and able to reproduce in adverse conditions in comparison to exotic sheep breeds. Therefore, the aim of this study was to determine whether there are any genetic mutations between indigenous breeds in known fecundity genes, growth differentiation factor 9 (GDF9) and bone morphogenetic protein receptor type 1B (BMPR1B/FecB), in four South African indigenous sheep breeds. A total of 52 blood samples were collected from four sheep breeds (Karakul = 8; Damara = 8; Zulu = 18; Pedi = 18). Unlabeled forward and reverse primers were used to amplify the GDF9 and BMPR1B genes. The PCR products were sequenced by a standard capillary sequencer. Sequencing results were analyzed using BioEdit, thereafter the detection of single nucleotide polymorphisms (SNPs), and phylogenetic analysis with the MEGA-X software. The results indicated that there are point mutations between sheep breeds in the GDF9 and BMPR1B gene compared to that of the Ovis aries complete coding sequence found in GenBank. Mutations of GDF9 gene (c.142C>T) and (c.151G>C) were detected in individuals of the Karakul, Damara, and Zulu sheep. The results also show that BMPR1B gene has mutation (c.80G>C) between individuals of the Zulu and Pedi sheep. Molecular phylogenetic analysis for both genes using the Neighbor-Joining method indicates relatedness between the Zulu and Pedi sheep. Damara breeds are more distantly related to Zulu and Pedi but show more relatedness with Karakul sheep. Polymorphism between and within the sheep breeds could be an indication of genetic variation that is potentially associated with higher prolificacy in indigenous sheep breeds.