The Firth of Lorn has been selected as a Special Area of Conservation (SAC) for the marine feature (reefs) an Annex I habitat under the 1992 Habitats Directive. The chief reason for the selection of this site is that the varied physical environment, with its complex group of islands, sounds and inlets characterised by some of the strongest tidal streams in the UK, is reflected in the great variety of reef types and associated communities and species which are amongst the most diverse in both the UK and Europe. The purpose of the current study was to initiate site condition monitoring of the intertidal and subtidal reef habitats within the SAC, establish a baseline biological data set that would facilitate the assessment of the condition of the reef habitats in the future and allow a judgement to be formed on the current condition of these habitats. A hierarchical biological sampling approach was adopted to achieve these aims. An extensive drop-down video survey of subtidal biotopes (habitats and associated species) was undertaken together with more detailed semi-quantitative and quantitative sampling of intertidal and nearshore subtidal reefs and their associated communities.