To meet demographic demand, global rice production will have to increase by about 2% per year despite losses of land and water supply to industrialisation and urbanisation, and the reduction of availability of farm labour. In Asia, the traditional transplanting of rice is increasingly being replaced by direct seeding that reduces labour costs and saves water. However, yield in direct seeded rice is threatened by weed competition due to the absence of weed suppression through early flooding. Moreover the appearance of "weedy" rice has notably been associated with the use of direct seeding. Weedy rice are plants that appear in and around rice fields and exhibit unwanted wild traits that reduce the quality and the quantity of the harvest. Little is known of the evolutionary origin of weedy rice. The aims of this project were to examine the phylogenetic relationships between weedy rice, cultivars, and wild rice to investigate the origins of weedy rice and to develop molecular diagnostics that would identify weedy rice contamination of seed sources. Using 19 microsatellite markers, individual plants of weedy rice, and cultivars from field samples in Malaysia and the Philippines were genetically characterised together with populations of Oryza niwlra and 0. rlljipogon, rice wild relatives. from different geographical locations in south east Asia, and reference 0. saliva accessions. Genetic differentiation between weedy rice and crop cultivars was evident. Weedy rice populations were more closely related to companion crop cultivars in Malaysia than in the Philippines. In the Philippines, weedy rice appeared to be genetically intermediate between crop cultivars and certain wild rice accessions, suggesting the presence of wild rice genes in their genomes. There are three main hypotheses for weedy rice: the invasion and persistence of preadapted annual wild rice in cultivated fields; the introgression and segregation of genes from annual or perennial wild rice surrounding fields into the sown cultivars; the segregation and expression of weedy traits introgressed during cultivar production. The data presented in this study demonstrated that weedy rice appears to be cultivars with introgressed wild traits. This excludes the first hypothesis. The fact that there is little or no evidence of 0. nivara and 0. rujipogon around the fields in the sampled regions also suggests that the second hypothesis is unlikely unless the source is cryptic. The conclusion of this study therefore has to be that weedy rice plants are "hybrids", carrying cultivar and wild traits. However, the use of 0. nivara in the breeding program of modern varieties to produce lines resistant to diseases may have accidentally introduced genes for unwanted wild traits (e.g. seed shattering, red peri carps, awns) to genomes of cultivars. These traits were subsequently selected against during the development of elite lines, but the release of highly inbred but not completely isogenic lines may allow the segregation and selection of these traits and hence produce weedy rice plants. The distant relationship between the weedy rice and the cultivars in the Philippines, allowed the identification of two genetic regions (one insertion in the microsatellite RM009, and one in the intron 2 of the catalase, CatA, gene) specific to weedy rice. These regions were used to design two PCR based molecular diagnostics that showed nearly 100% correlation between a PCR amplification and the presence of a weedy phenotype. The close genetic relationship between cultivars and the weedy rice samples in Malaysia prevented the identification of such regions.