Macroalgae is one of the Biological Quality Elements (BQE) used by several indexes conceived in the European Water Framework Directive (WFD) for the assessment of the Ecological status of coastal water bodies. Among them, CARLIT index, based on the cartography of rocky-shore littoral communities, has been extensively and successfully applied in the Western Mediterranean Sea. In this study CARLIT was applied for the first time in the Levantine Sea, along the Lebanese shoreline in order to test the suitability of this method in the peculiar ecological conditions of the Levantine Sea and have a first assessment of its ecological status. The choice of proper reference sites is a focal point in the fulfillment of the WFD. In order to ensure accurate calculation of the ecological status of the Lebanese coast, the calculations of the reference conditions (RC) were performed using the values calculated in the Lebanese reference area, the Northwestern (NW) Mediterranean RC proposed in the first application of the CARLIT method and the Adriatic Sea RC. The results showed that the calculated ecological quality ratio values (EQR) based on Lebanese RC is particularly important when considering the principle of the WFD to reach and maintain a good Ecological Status. Overall, the EQR values were well correlated with anthropogenic pressures, as assessed by the LUSI and MA-LUSI indexes. In addition, this method allowed the collection of accurate information on the distribution and abundance of shallow-water communities, especially of those deserving protection (e.g. Cystoseira forests). Thus, the present paper represents a baseline for future studies and gives useful tools for the management of human impacts on the Lebanese coast.