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Diatoms are good environmental indicators and are often the main component of phytobenthos, one of the key groups of organisms recommended by the Water Framework Directive (W.F.D.) for the assessment of ecological status of surface waters. Although diatoms are regularly used as indicators in rivers and in lakes, less is known about the benthic diatom communities in wetland systems, especially in Italy. The main aim of the project was to provide a contribution to the knowledge on distribution, composition and structure of benthic diatom communities in wetland systems in Italy. In 2005, we investigated the benthic diatom communities and their relationships to water variables of nine ponds and wetlands along the Tyrrhenian coast near Rome. Furthermore, a first application of seven European diatom-based indices on this type of water body was undertaken. A total of 225 species and varieties belonging to 54 genera were identified. The Canonical Correspondence Analysis indicated that certain species were closely associated with each wetland type and their distribution mainly depended on nutrient and chloride contents: pollution tolerant species (i. e. Luticola goeppertiana, Mayamaea atomus, Navicula subminuscula) in the wetlands connected to river mouths, halophilous species and also marine littoral species (i. e. Nitzschia elegantula, Amphora coffeaeformis, Achnanthes brevipes var. intermedia, Epithemia adnata var. porcellus) in the coastal brackish ponds and wetlands, and less eutrophic species (i. e. Achnanthidium minutissimum, A. biasolettianum) in the lowland freshwater wetland. In general, the indices classified most of the studied water bodies as bad, poor and moderate status; few sites were classified into a good class, even for at least in one sampling occasion. Eutrophication and Pollution Index (EPI-D), Trophic Diatom Index (TDI), Taxa Pollution Tolerant (%PT), Pollution Sensitivity Index (IPS) and Generic Diatom Index (IDG) were significantly correlated to nutrient contents in the studied wetlands. Our preliminary data set illustrated the potential of the use of these benthic algae as bioindicators in wetlands.