The distribution and abundance of many coral reef organisms are affected by their predator’s distribution and abundance. Loss of predators may cause a shift in species compositions that will cascade down to other ecological processes on the reef. One example of a shift like this is the growing sea urchin populations inhabiting the coral reefs of East Africa. Areas with high fishing pressure often have large populations of sea urchins. The large populations of sea urchins have a negative impact on the reef ecology both by their grazing and bio-erosion as well as on fish growth and the recovery of fish populations. Previous population genetic studies conducted on Diadema setsosum, using mtDNA and allozymes, found genetic structuring between populations on a large geographical and evolutionary scale. The aim of this study was to examine the genetic population structure of the sea urchin Diadema setosum, at four sites around Zanzibar. We used the amplified fragment length polymorphism (AFLP) technique, a fast and effective method with high resolution. The long term objective is to understand the migration pattern and colonization of D. setosum to facilitate possible management actions. We found a significant genetic structuring of D. setosum hence the populations can not be considered panmictic. The reason behind this structure does not seem to be based on the geography nor size. One possible explanation might be that the structure lies on a larger geographical scale than we have studied, further studies around the Western Indian Ocean may reveal this. Another explanation may be that the structuring is due to differences in spawning time between the different phenotypes and an analysis of gonad maturations may give information about this. To find the reasons behind the observed genetic structure is of great importance for management of the sea urchins and therefore the management of whole reef ecosystems.