Display omitted •Changes in the structure and abundance of macroalgae.•Long term decline in the number of canopy-forming algal taxa.•Critical loss in the coverage of canopy-forming algal taxa.•Shifts from canopy-forming to turf-forming algal taxa. Canopy-forming macroalgae, especially those belonging to the order Fucales, are creating the so-called brown algal forests that are considered amongst the most productive assemblages in the shallow coastal area. Moreover, they are biological indicators that are used for the assessment of the status of coastal belts according to important European Directives. Along Mediterranean rocky coasts they are disappearing quickly, Cystoseira species (sensu lato) in particular, and are gradually being replaced by turf-forming smaller and persistent algae, due to multiple anthropogenic pressures. The scope of this research was to verify changes in macrophyte structure and abundance, especially canopy-forming taxa, and the loss of Cystoseira s.l. species at two reference sites for macroalgae in the northern Adriatic Sea, during the period 2007–2019. At both sites, the decline of total Cystoseira s.l. spp. coverage (%) was substantial, both in the spring and autumn samples, while some rare and sensitive species were not found during the last surveys. The results of this study should help improving the conservation status of important canopy-forming species, focusing on the revitalisation of benthic critical habitats.