An almost unbroken fringing reef runs along the east coast of Africa, the lagoon inside the reef is the foundation of almost all artisanal fisheries. It is a low-tech fishery conducted by many people. Some areas can have up to 19 fishermen per square kilometer. High fishing pressures, coupled with declining fish stocks has led to changes in mean size and reproductive age of many exploited species. There is a vital and urgent need for scientifically based management systems, including the utilization of genetic information to guide management practices. This thesis aims to investigate the presence of genetic structures in the western Indian Ocean. In order to do that we first investigated the historical patterns of connectivity throughout the region (paper I). In papers II and III we focused on local scale connectivity in Kenya and Tanzania and finally in paper IV we investigate the large-scale contemporary gene flow throughout the Western Indian Ocean. In paper III we also investigate the temporal genetic variation at one site and compare it to the small-scale genetic variation along a stretch of the Kenyan coastline. Some overall conclusions that can be drawn from my body of work are: there are genetic structures present in the western Indian Ocean even though the apparent lack of physical barriers. Major oceanic currents aid evolutionary dispersal patterns. A single geographic site need not be genetically homogenous or temporally stable. Island sites are genetically more homogenous than mainland sites. In conclusion, there are clear and distinct genetic structures present especially in Siganus sutor, the most targeted fish for the artisanal fishery in East Africa. / <p>At the time of the doctoral defense, the following papers were unpublished and had a status as follows: Paper 3: Manuscript. Paper 4: Manuscript.</p>