Coral reefs are some of the most diverse and important ecosystems on earth. These ecosystems are highly important as nurseries for a large number of marine flora and fauna, tourist attractions, and as sources of medical compounds. The health of these reefs depends on the population balance of algae, sea urchins, fishes and other marine organisms. Overpopulation of any species can disturb this balance and negatively affect the reefs. Overgrazing by sea urchins damages the coral reefs. Investigations have demonstrated a considerable increase in sea urchin populations in the coral reefs in Khark and Kharku islands. This research aims to discover the reasons for the increase in the population of sea urchins, its impacts on coral reefs in Khark and Kharku, and propose strategies for dealing with this problem. To achieve these aims, 7 stations were chosen. Subsequently, density, reproduction, and nourishment of sea urchins were investigated monthly for each of these stations. Morphological and molecular identification of urchins were performed and coral and floral coverage and fish population were examined for each station. Physicochemical parameters of water were also studied in order to determine the concentration of TOC, heavy metals, PAHs and microbial pollutions. The statistical data concerning the fish species were obtained through distributing questionnaires among local fishermen and also the data provided by Bushehr Fisheries Administration. Morphological examinations showed that the present sea urchin species in the area is Echnometra mathaei and molecular analysis confirmed this. As for the population density, it turned out that it was way above the global average. It was found that through feeding on corals, as their primary source of nourishment, sea urchins have caused substantial damage to the reefs. The analysis of the sea urchin reproduction indicated that they spawn in hot months (June and July). However, it was discovered that in the fourth station they