The aim of this study was to initiate site condition monitoring (SCM) of the littoral and sublittoral reefs and sea caves within the Mousa SAC. The purpose of this SCM is: 1) to establish a baseline biological data set that will facilitate the assessment of the favourable condition status of the habitats in the future; and 2) to allow judgement on the current condition of the habitats in the light of existing SAC management measures. To fulfil these objectives an extensive drop-down video survey of the sublittoral reef habitats of the SAC was completed in conjunction with detailed MNCR phase 2 surveys of reef biotopes along relocatable transects spanning both the littoral and inshore sublittoral environments. Sea cave distribution was examined, and for selected caves, the topography was mapped and the biotopes surveyed at relocatable points within five selected caves along the cave system.