Glen Affric, a National Nature Reserve of international conservation importance for plant and animal communities associated with Scots pine (Pinus sylvestris) woodland is managed for nature conservation and woodland restoration at a landscape scale. Management plans have drawn on information on current stand structure and variation but have not used in any detailed way the analyses of past tree population changes from sources, such as pollen analyses. This paper reports the results of pollen analyses from three small peat hollows at the head of Loch Beinn a' Mheadhoin. The analyses demonstrate, first, that woods in the east of the reserve several centuries ago were different in species composition and were more varied than they are today and, second, that the currently patchy Pinus wood in the west of the reserve, at the head of Loch Beinn a' Mheadhoin, is the result of recent spread westward onto former heathland. This temporal and spatial variability in the recent past has implications for the future management of the woods because future woods may not develop with the characteristics of the current stands, and may not be stable over time.