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Indicators are key tools used to assess the ecological status of the environment for ecosystem based management. Anthropogenic disturbances produce changes to habitat condition, which include modifications in species composition and their functions. Monitoring a group of sentinel species (from a taxonomic and functional point of view) provides useful insights into benthic habitat condition. Here, a new indicator, Sentinels of the Seabed (SoS) is proposed to assess state of benthic habitats using “sentinel” species (species which are characteristic of a habitat and sensitive to a given pressure). The selection of these sentinel species has two stages. First, a ‘typical species set’ is computed using intra-habitat similarity and frequency under reference conditions. Second, the ‘sentinel species set’ is generated by selecting the most sensitive species from the typical species set. This selection is made using specific indexes able to assess species sensitivity to a particular pressure. The SoS indicator method was tested on six case studies and two different pressure types (trawling disturbance and pollution), using data from otter trawl, box-corer and Remote Operate Vehicle images. In each scenario, the SoS indicator was compared to the Shannon-Wiener diversity index, Margalef index and total biomass, being the only metric, which showed the expected significant negative response to pressure in all cases. Our results shows that SoS was highly effective in assessing benthic habitats status under both physical and chemical pressures, regardless of the sampling gear, the habitat, or the case study, showing a great potential to be a useful tool in the management of marine ecosystems.