The following is a list of Sites of Special Scientific Interest in the Western Isles South Area of Search. For Western Isles North see List of SSSIs in Western Isles North. For SSSIs elsewhere in Scotland, see List of SSSIs by Area of Search.
- Allt Volagir
- Baleshare and Kirkibost
- Balranald Bog and Loch nam Feithean
- Berneray
- Boreray
- Bornish and Ormiclate Machairs
- Eoligarry
- Howmore Estuary, Lochs Roag and Fada
- Loch an Duin
- Loch Bee
- Loch Bee Machair
- Loch Druidibeg
- Loch Hallan
- Loch nam Madadh
- Loch Obisary
- Lochs at Clachan
- Machairs Robach and Newton
- Mingulay and Berneray
- Mointeach Scadabhaigh
- Monach Islands
- Obain Loch Euphoirt
- Pabbay
- Rockall
- Small Seal Islands
- St Kilda
- Vallay
- West Benbecula Lochs