This study determined the occurrence and frequency of mutations that influence performance traits in the SA Boerperd horse and evaluated genetic diversity within the breed. Two gait-associated and two height-associated mutations were investigated. Seventeen microsatellite markers were genotyped for 363 horses and used to assess genetic diversity. The C-allele of the height-associated single nucleotide polymorphism (SNP) BIEC2_808543 was present in 5% of the population, and 57% of the horses possessed the A-allele of BIEC2_1105377, which has been also associated with height. However, these SNPs did not significantly affect measured phenotypic height within the breed. The minor alleles for SNP DMRT3_Ser301STOP and BIEC2_620109, which have been associated with gaitedness, occurred with frequencies of 0.105 and 0.091, respectively, within the breed. The microsatellite data revealed observed heterozygosity (Ho = 0.679) to be similar to that found 15 years ago, while the level of inbreeding had decreased from 8.4% to 3.2%. However, allelic richness had declined from 4.212 to 3.804. Analysis of the population structure revealed that two distinct founder populations have contributed to the present-day breed. Compared with nine European breeds, the SA Boerperd had above average levels of heterozygosity and a high number of private alleles (17.6%). A high degree of variation remained in the SA Boerperd, despite selective breeding, and levels of inbreeding were still manageable. Results obtained in this study can be used by SA Boerperd breeders to develop the breed, while simultaneously conserving its genetic potential.