Abstract The microalgal community of benthic mucilages sampled in various sites of the Tuscan Archipelago during the period May 1999–July 2002, was always dominated by diatoms. Synedra, Licmophora and Navicula were the most frequently found genera, their presence having been observed within all the period under study; other ten genera of diatoms were found in the benthic mucilages, but their presence was dependent on the month and the year of observation. As concerns the cyanobacterial community, the filamentous genera Leptolyngbya, Lyngbya and Rivularia were the most frequently found, independently on the period and the year of samplings, while other genera, namely Oscillatoria, Symploca, Aphanocapsa and Gloeocapsa, were less frequently observed. During the period under study, the highest number of different genera of diatoms and cyanobacteria in the mucilaginous aggregates was observed during summer periods, particularly in June and July. The microscopic observation of the samples demonstrated that only diatoms belonging to the genera Navicula, Amphora, Cylindrotheca and Pseudo- nitzschia possessed outermost polysaccharidic investments, the cells of the other genera being devoid of sheaths or capsules. On the other side, all the observed cyanobacteria, with the exception of Oscillatoria strains, were characterized by the presence of outermost polysaccharidic investments, most frequently in the form of sheaths. However, when the microalgal and cyanobacterial isolates were cultured under laboratory conditions, the release of polysaccharidic material into the culture medium was observed only in a few cases and always in very small amounts. The observations done on the natural samples and the results obtained with the cultures of the microalgae and cyanobacteria isolated from the benthic aggregates suggest that only diatoms have given some contribution to the formation of the polysaccharidic material constituting the matrix of the mucilages, whereas the role of cyanobacteria in the benthic aggregates seems to be related to their capability to create biofilms on solid surfaces, constituting the first step in the colonization of the benthic surfaces by the microbial community.