Maërl beds are biogenic benthic habitats distributed worldwide and known to sustain high productivity and biodiversity levels. In the Mediterranean, the number of studies that have been carried out is limited, and little is known on its real distribution. In Greek marine sector the available information regarding the maërl beds is limited and scattered. They are vulnerable to physical disturbance by fishing gears and smothering, and to water pollution by organic enrichment and sewage. Although maërl beds are protected by EU legislations and directives the lack of maps and information on their distribution makes the effective application of these measures impossible. This work concerns the potential impact of aquacultures in maërl beds in Eastern Mediterranean in order to propose a management and a conservation plan for its protection.