The maternal lineages and origins of the South African goat populations are unknown and hence pose challenges for breed characterization and conservation. This study investigated the maternal lineages of South African goats using complete mtDNA and ascertained the genetic diversity in the growth hormone gene within and between populations. Illumina MiSeq next generation sequencing was used to generate the full length of the mtDNA (16.64 kb) and growth hormone (2.54kb) genes in 50 goats of the commercial South African Boer (n =9), captive feral Tankwa (n =9), and SA village goat populations (n =32). The non-descript village populations were sampled from villages of the four major goat-producing provinces; (i) Hobeni village, Elliotdale municipality and Pechelsdam village, Inxubayethemba municipality in Eastern Cape (n=8), (ii) Coniliva and Ngubo villages in Msinga municipality Kwa-Zulu Natal (n=8), (iii) Mukovhabale village, Mutale municipality and Muila-muumone, Makhado municipality in Limpopo (n=8) and (iv) Pella village (n=6), Moses Kotane municipality North West (n=8) provinces of South Africa. A total of 184 SNPs and 55 AA changes were observed across the complete mtDNA genome. High within-population variation was observed in all the groups, ranging from 98.60 to 99.52%. A low FST (FST = 0.003-0.049) indicated close relatedness and possible gene flow between SA goat populations. Haplotypes and clades observed in the D-loop, COX1 and whole mtDNA network trees demonstrated relationships between South African goat populations. The South African goats clustered with Chinese goats from lineages A and B, suggesting common maternal lineages between the Chinese and South African goat populations. The results also suggested that the bezoar (Capra aegagrus) is a possible ancestor of South African domestic goats. A range of 27 to 58 SNPs per population were observed on the growth hormone gene. Amino acid changes from glycine to serine, tyrosine to cysteine and arginine to glycine were observed at exon 2 and exon 5. Gene diversity ranged from 0.8268 ± 0.0410 to 0.9298 ± 0.0050. Higher within breed diversity (97.37%) was observed within the population category consisting of SA village ecotypes and the Tankwa goats. Highest pairwise FST values ranging from 0.148 to 0.356 were observed between the SA Boer and both the SA village and Tankwa feral goat populations. The maximum likelihood phylogenetic analysis indicated nine genetic clades, which reflected close relationships between the South African populations and the other international breeds. Results imply greater potential for within population selection programs particularly with SA village goats. / Life and Consumer Sciences / M.Sc. (Statistical Genomics)