It is accepted that observed patterns in community structure change as analyses are carried out at higher taxonomic levels. Univariate analyses which incorporate higher taxonomic structure within assemblages have been shown to be informative. In this paper we suggest ways in which changes in multivariate relationships at higher taxonomic levels and associated with higher taxonomic/phylogenetic structure of the community may be incorporated into multivariate analyses, an aspect never occurred before in this type of analysis. Four approaches, namely: biodiversity MDS (bdMDS), number of taxa MDS (ntMDS), delta MDS (δMDS) and lambda MDS (λMDS), are proposed, and applied to theoretical data as well as to data collected from the literature on the Mediterranean lagoonal environment. Results show that these approaches have the capacity to distinguish severely impacted lagoons from naturally disturbed ones, although in practice the simplest method (ntMDS) was the most successful. Analyses based on the most abundant groups (polychaetes, molluscs, crustaceans) did not always match analyses based on the entire macrofauna, mirroring the performance of taxonomic distinctness indices in the Mediterranean lagoons. The important characteristics of the approaches introduced, as well as potential criticisms are provided. Application of these techniques on smaller scales and to other habitats, is suggested prior to their wider use in the region.