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There is a strong scientific consensus that coastal marine ecosystems, and in particular the midlittoral zone, at the interface between terrestrial and marine realms, are seriously threatened by anthropogenic impacts, along with the goods and services they provide. Along Mediterranean shallow rocky reefs, brown macroalgae belonging to the Cystoseira genus (e.g. Cystoseira amentacea and Cystoseira compressa) are ecosystem engineers, locally creating a continuous fringe in the midlittoral zone, supporting high biodiversity and productivity and providing ecosystem services. A growing interest in the quantification of ecosystem relevance through their economic value aims at raising public awareness and supporting policy-makers in the process of creating new legal instruments supporting the preservation of biodiversity. In this framework, a methodology for ecological and monetary evaluation of natural capital, based on biophysical accounting and on emergy theory, is applied to the habitats of the upper midlittoral zone located above continuous and non-continuous Cystoseira fringe. The proposed approach is a quantitative measure able to analyse the overall functioning of the system and its efficiency in exploiting available resources. The mean economic value of the habitats in the midlittoral zone assessed through the present study is 1.28 emE/m(2). Higher values, but associated with a larger variability, were observed in presence of continuous C. compressa fringe. Conversely, in the presence of a continuous C. amentacea fringe, a noticeable habitat-forming species, lower natural capital values were recorded possibly due to the attractive potential of this species in its understorey rather than in the above habitats, concurrently with a lower variability of the natural capital values (lower scatter), suggesting a deterministic homogeneity effect on the above midlittoral habitats. From this study, emergy analysis is confirmed to represent an effective and operative tool to provide a synthetic monetary assessment of natural capital making complex information easily accessible to different stakeholders, from general public to territorial managers.