South Africa is considered the primary producer and most reliable source of high quality clip mohair in the world. The application of molecular technologies to improve mohair quality is relatively new to this industry. The aim of the study was to use a molecular approach to genetically improve South African Angora goats, with emphasis on mohair production. A reference population of Angora goats was firstly established consisting of twelve sire families with half-sib offspring (1067 individuals in total). The genetic variation of this population was evaluated using microsatellite markers and the average gene diversity was found to be above 60%. Ninety four microsatellite markers were then genotyped on the reference population, spanning 23 chromosomes (total length 1352cM) with an average marker interval of 23.0cM. This information was used to improve previously published goat linkage maps. Unmapped microsatellite markers were incorporated and previously published inter-chromosomal rearrangements between the goat and sheep genetic maps were confirmed or rejected. Nine new markers were mapped to the goat genome, and six chromosomes showed rearrangement when compared to the previous goat map. Four previously reported intra-chromosomal rearrangements were shown to be either population specific or mapping errors. Variance components and genetic parameters of mohair traits (FW, FD, CVFD, SDFD, CF, SF and SDA) were estimated; including the fibre diameter profile measured using OFDA technology that has not yet been included in genetic evaluations. Heritability estimates ranged between 0.14 (SDA) and 0.63 (CF). OFDA-measured traits should be considered for inclusion into the national breeding strategy. The reference population was lastly analysed to identify QTL associated with fleece traits. Eighteen putative QTL were identified for seven mohair traits on 13 chromosomes. Three putative QTL were detected for FW on CHI 2, 5 and 24 corresponding with KRT and KAP gene locations. Two QTL associated with mohair FD (on CHI 4 and 24) were detected. QTL contributions to variance ranged between 7.44% (CF) and 19.69% (SDA). The results of this study should form part of an integrated approach where both quantitative and molecular tools are applied for genetic improvement of South African Angora goats.