In this study, the use of reduced assemblages of benthic invertebrate taxa is proposed to describe similarity relationships between samples from transitional environments. A data set from four different studies, made up of 641 samples for a total 203 species, was analysed using permutation randomisation tests in order to extract a pool of taxa able to approximate the full set of species. The identified "operational set", comprising 19 taxa, was capable of adequately reproduce similarity relationships between samples (Rho>0.90, p<0.001). All selected taxa were easily extractable from the samples and easy identifiable by non-specialised technicians; these characteristics were considered appropriate for the development of rapid and cost-effective monitoring procedures based on benthic invertebrate assemblages.