The distributions of the pennatulid anthozoans (sea pens) Virgularia mirabilis, Pennatula phosphorea and Funiculina quadrangularis in Scottish waters have previously only been extensively documented in sea lochs, by the Marine Nature Conservation Review (MNCR) surveys. Funiculina quadrangularis in particular was thought to be restricted to the deep basins of sea lochs and is classified as a nationally uncommon species. Sea pens are characterizing species in seven biotopes found in Scottish waters and are protected under the ‘Mud in Deep Water Habitat Action Plan’ of the UK Biodiversity Action Plan (UKBAP) and are also recorded in several Special Areas of Conservation. The present study has extended the existing information available on sea pens in Scottish waters. The distribution and abundance of the three sea pen species were mapped using GIS (Geographical Information System) by utilizing data from Nephrops norvegicus stock assessment video surveys carried out by Fisheries Research Services (FRS) Marine Laboratory. Distribution was shown to be aggregated for all species. Funiculina quadrangularis was present in areas outside the sea lochs, such as the South Minch and the outer mouths of most sea lochs. This study demonstrates that analysis of video footage derived from Nephrops stock assessment surveys can significantly extend our knowledge of sea pen distribution and population density. Future management of Nephrops stocks can be expected to consider impacts of fishing on non-commercial species such as sea pens as a part of the ‘ecosystem approach’ to management.