The sea pens Funiculina quadrangularis, Pennatula aculeata, Pennatula phosphorea, Pteroeides spinosum and Veretillum cynomorium are known to be characteristic species of the habitat ‘pennatulacean communities on circalittoral and upper bathyal soft bottoms’, described recently on the northern Atlantic Spanish shelf under the terms of the EU directives. Distribution, abundance and environmental data collected from 1995 to 2010 in the Northern Spanish Shelf Groundfish Surveys in the Cantabrian Sea and off Galicia (SPNGFS) were analysed. Although low densities of sea pens were commonly found over the years, some aggregations were shown. Multivariate analysis separated the aggregations of F. quadrangularis and of Pennatula spp. found on circalittoral soft bottoms. In addition, evidence of aggregations of F. quadrangularis on upper bathyal sites was also found. Depth and longitude, which were closely related to organic matter and sediment particle size, were key factors in determining the distribution and abundance of these aggregations. However, very little information on distribution and density of the species P. spinosum and V. cynomorium was obtained. Details of community composition of F. quadrangularis and Pennatula spp. were studied and compared with those of the OSPAR habitat “sea pen and burrowing megafauna communities” in other areas. The results improve our knowledge concerning sea pen communities in the southern Bay of Biscay and contribute to a global assessment of the status of these communities in the northeast Atlantic.