Biodiversity conservation and response of benthic communities to pressures, related to global change and human activities, are a research priority. They also constitute a useful indicator to define the environmental status of the Marine Strategy Framework Directive as part of the European Water Framework Directive (WFD). The biogeographic features of the Aquitanian coast (in terms of rocky substrate communities) induce the interest to have a monitoring and research site. Indeed, it includes the habitat characteristics as well as fauna and flora (the Habitats Directive). The aim of the BIGORNO project is to implement new tools to assess the rocky biocenosis in the southern marine subregion of the Bay of Biscay by integrating fauna communities assessment (flora communities already monitored in WFD). This provides further information about the intertidal biodiversity and the spatial distribution of benthic communities. A standardized procedure for collecting information on benthic communities provides relevant indicators of intertidal habitat. Global environmental change (including climate evolution) should be considered while entering these indicators in European framework in order to compare results over longer periods. Using a spatially stratified random sampling plan, the mobile fauna (true abundance), fixed fauna and macroalgae (percentage cover) were measured in quadrats of 0.1 m² spread both on upper and lower mediolittoral zones. The analysis highlight dependent faunistic and floristic structuration according to microhabitats which confirms the need of a such stratification. Species/taxa or species associations were also identified as indicators of microhabitats. These various analysis improve knowledge for monitoring the Basque intertidal rocky shore in a sustainable way. Finally, within the Marine Strategy Framework Directive, these results allow to take into account biogeographic specificities to harmonize protocol metrics at the scale of the sub-area Bay of Biscay.