The CARLIT methodology is an Ecological Quality Ratio (EQR) widely used in the Mediterranean Sea to assess the ecological status of coastal water bodies, within the framework of the European Water Directive (European Union, EU) of 2000. It is based upon the exhaustive mapping of a set of mid-littoral and shallow infralittoral species and communities. This methodology was applied, for the first time in a non-EU country, Albania, three years after the establishment of a Marine Protected Area (MPA). The observed range of ecological status was wide (‘high’ through ‘bad’) and was overall among the lowest assessed to date in the Mediterranean Sea. The bioconstructions (algal rims) edified in the lower mid-littoral zone by the calcified rhodobiont Lithophyllum byssoides were in poor condition and sometimes even dead, possibly in relation with the pollution and the on-going global sea-level rise. In addition, Cystoseira amentacea, a brown alga whose weight in the index is high, could be less sensitive to pollution than previously expected. The occurrence of extensive sea-urchin barren-grounds, though not taken into consideration by the CARLIT index, confirmed the poor condition of large sectors of the study area. Overall, the assessed ecological status could prove to be overestimated by the CARLIT methodology and some methodological improvements should therefore be considered.