The Water Framework Directive (WFD) 2000/60/EC, adopted by the European Community in 2000 with the goal of maintaining and improving the aquatic environments, requires that member states achieve and maintain a good ecological status of all water bodies by 2015. In the marine context, the ecological status has to be quantified applying indexes based on appropriate key biological elements, which allow the categorization of water bodies into five Ecological Status (ES) classes. The CARLIT index is a cartographic monitoring tool enabling the Ecological Quality Ratio (EQR) to be calculated using macroalgae in coastal hard bottoms as a key biological element; at present it is being applied in Spain, France and Italy. To detect actual changes of water quality and, consequently, rely on the application of indexes for the assessment of the ecological status in the marine environment, it is necessary to evaluate their sensitivity to natural variability at different temporal and spatial scales. In this study we present a first quantification of natural (spatial and temporal) variability of EQR-CARLIT quality assessment in 2006 and 2007 along the Ligurian coast (North-Western Mediterranean, Italy). The EQR-CARLIT values recorded along the Ligurian coastline show that natural variability of EQR-CARLIT is low and that it does not affect the attribution of a given stretch of coast to a particular ES class, in agreement with the major human pressures acting in the area (urbanization, river load, sea-farming). A small-scale variability was detected, strengthening the use of cartography of the whole rocky shore, whenever possible, or, alternatively, the assessment of the ecological status for long stretches of coast, to encompass the small-scale variability due to local factors.