We applied a multifaceted approach, in terms of taxonomic, phylogenetic and functional diversity, to study at fine scale how three plant communities occurring in a Mediterranean dune have been affected by the encroachment of alien species. We sampled 81 sites in a Site of Community Importance in Central Italy. Past and present land use/cover data have been derived using GIS and remote sensing tools. Information on plants phylogenesis and functional traits has been gathered from several databases. Ecological variables have been collected. GLMs in conjunction with an Information Based approach were used to model species composition, richness and phylogenetic diversity. Multivariate analysis has been used to study functional diversity. The results outlined how total species richness is related to recent land transformations and to a set of environmental factors. The analyses of functional and phylogenetic diversity support the idea that alien species significantly affect the functional and phylogenetic characteristics of the native plant communities. Habitat filtering seems to be predominant in not-invaded plots, whereas limiting similarity/niche differentiation is predominant in driving community assembly of invaded communities. The attained scenario depicts the spread of a reduced group of alien species phylogenetically and functionally well-differentiated, able to reduce the abundance of native species, not to exclude them though. Ultimately, the multifaceted approach assisted in understanding the community assembly of dune vegetation, and to discern the relative impact of alien species on native plant communities. Such approach represents a crucial step to achieve an efficient management of dune habitats, as useful tool to monitor and to effectively protect their biodiversity and functioning. © 2014 Springer Science+Business Media Dordrecht.