Grey seals, Halichoerus grypus, around the west Wales coast are the most southerly breeding population in Europe of one of the least common seal species. The seals utilising the area of the Pembrokeshire Marine SAC comprise the major proportion of an isolated breeding population, in which the breeding ecology differs from that of grey seals elsewhere. The West Wales population size, as determined by pup production estimates, is approximately 5000 individuals. This represents c.4% of the UK population and c.2% of the world population of grey seals.

Grey seals breed on undisturbed beaches of cobble and boulders, and on cobble beaches within sea-caves along the coast. Pupping time occurs primarily from August through to December with September generally being the busiest month. Pups tend to be born earlier on Ramsey than they are on Skomer. After three weeks the white coated pups have moulted and are ready to fend for themselves. Adult seals congregate in large numbers on beaches between December and February to moult.

Grey seals can be found within the site throughout the year, particularly obvious at low tide when they can often be seen ‘hauled out’ on the rocks. The best places to see seals are the offshore islands, although they do venture within the Milford Haven waterway and have been seen feeding within the Daugleddau. Stack Fort is a popular haul out site.

Grey seals are afforded some seasonal protection by the Conservation of Seals Act 1970 (as amended). They are a local Biodiversity Action Plan species.