[Truncated abstract] Narrow-leaf lupin (Lupinus angustifolius L.) was first recorded as having been introduced into Germany during the mid-19th century for use as green manuring and as fodder crops. However, it was not until post World-War I that there was any serious attempt to domesticate the species. Since that time several key domestication genes have been incorporated to enable the species to be grown as a crop over a range of climates, harvested as a bulk commodity and, the seed used for both animal and human consumption. However, the recent domestication of this species has seen a rather limited use of wild germplasm largely as a result of the difficulty in retaining these key domestication genes. To make the task of retaining these genes manageable, it was decided to resort to molecular technology. A mapping population of F8 derived recombinant inbred lines (RILs) has previously been established by the Department of Agriculture and Food, Western Australia, from a cross between a domesticated breeding line 83A:476 and a wild type P27255 in narrow-leaf lupin. The parents together with 89 RILs (of a population of 115) were subjected to DNA fingerprinting using microsatelliteanchored fragment length polymorphism (MFLP) to rapidly generate DNA markers for construction of a linkage map. Five hundred and twenty two unique markers of which 21% were co-dominant, were generated and mapped. Phenotypic data for the domestication traits: mollis (soft seeds), leucospermus (white flower and seed colour); Lentus (reduced pod-shattering), iucundis (low alkaloid), Ku (early flowering) and moustache pattern on seed coats; were included. Three to 7 molecular markers were identified within 5 cM of each of these domestication genes. The anthracnose resistance gene Lanr1 was also mapped. Linkage groups were constructed using MapManager version QTXb20, resulting in 21 linkage groups consisting of 8 or more markers. ... Five pairs of QTLs were found to be involved in epistasis, 2 of these having an effect on early vigour and another 3 influencing the time to opening of the first florets. Variation explained for each trait ranged from 28% for seed size, to 88% for days to flowering. We showed that it was possible to use this data to predict genotypes of superior progeny for these traits under Mediterranean conditions. QTL regions were compared on a second published linkage map and regions of conserved synteny with the model legume Medicago truncatula high-lighted. The work presented in this thesis demonstrates the importance of tight linkage between markers and genes of interest. It is especially important when dealing with genetically diverse material as found in the wild. One of the main problems faced by molecular scientists is the phenomenon known as linkage disequilibrium in marker populations caused by either small population size or 4 insufficient opportunity for recombination. This frequently results in the development of markers with little or no application outside of the population in which it was developed. Although the relatively small size of the population used in this study exposes it to such constraints, in this case excellent and valuable results were achieved in developing useful markers to at least 3 of the domestication traits within a relatively short time period of less then 4 years.