To implement the European Directive on conservation of natural habitats (92/43/EEC), government conservation agencies, in this case Scottish Natural Heritage (SNH), must identify areas as possible Special Areas of Conservation (pSACs). To inform the future management and monitoring of these sites, SNH need to know the distribution of habitats and species in Scottish marine SACs. Distribution of marine benthic biotopes (habitats and their associated species) was predicted for two physiographically different pSACs in Scotland: Papa Stour in Shetland, and Lochs Duich, Alsh and Long, NW Scotland. The methodology involved acoustic remote sensing, ground validated by remote video and grab sampling, with analysis and display of results using a PC based GIS. Field surveys were carried out in 1996. Acoustic track point data obtained were interpolated to obtain a continuous polygon coverage of the acoustic properties of the seabed within each pSAC area. An acoustic signature for each biotope type, or biotope complex was determined by buffering the ground validation sites, intersecting buffers with acoustic track data, and deriving descriptive statistics for each acoustic variable. Spatial analysis of acoustic and ground validation data within the GIS was then used to produce a continuous coverage polygon map of predicted biotope types for each pSAC.