Biodiversity is recognised as one of the main factors causing ecosystem stability and the existence of several ecosystem functions. In consequence, species richness can be a reliable state variable, useful to assess an ecosystem status or to identify highly valuable areas in a landscape. Here we present two applications in which species richness assessment allowed respectively the boundaries redesign of a part of the Natura 2000 network and an ex-post BACI (Before-After-Control-Impact) assessment as enforced by an infringement procedure for action against Article 4 of the Birds Directive. In the first case study, the boundaries of 16 Natura 2000 sites were redefined, identifying genuine scientific errors and expunging low species richness areas and incorporating high biodiversity areas whose value was not possible to assess when the sites were instituted. The overall balance involved a minimal surface area change (+1.5% SPAs, +1.6% SCIs) but a net gain in high quality habitats in the redesigned sites network. The second case presents a small scale a posteriori impact assessment, where an exact quantification of habitat and species loss allowed not only reporting the European Commission as requested, but also to individuate a new Natural Reserve with identical ecological traits as measure of compensation, positively resolving the pending infringement procedure.