The structure of the necto-benthic fish community and its relationship with habitat features was investigated for the first time by visual census in the protected area of the Lastovo Islands and the island of Mljet. Habitat type and rugosity were recorded by visual approximation. Fish assemblage data were collected by the method of underwater visual census on seven habitat types, which were summarized into four basic habitats for data analysis: (i) infralittoral algae communities, (ii) infralittoral alge with posidonia paches, (iii) half ratio of algae and posidonia and (iv) posidonia meadows with infralittoral algae patches. The structure of the necto-benthic fish community corresponed to a certain level to the habitat type. The highest species richness, abundance and biomass was recorded at the habitats of the infralitoral algae community with patches of posidonia, at the same time the smallest was recorded in the posidonia meadows. Influence of the habitat rugosity was not proven to affect the structure of the fish community. This study provides a basis for assessing the effectiveness of the „no-take“ zones planned in the investigated marine protected areas. Assesments of effectivness will be possible because the selection of control stations has been positively evaluated for most stations within NP Mljet planed for the "no-take" zone. Most control stations were similar in habitat and current qualitative and quantitative fish structure as stations in future „no-take“ zones.