On the Estonian islands the woodlands have been used as pastures, hay meadows or temporary fields throughout the history of human settlement. Signs of earlier traditional agricultural practices stretching back centuries may be found in the plant cover and soil characteristics of forest ecosystems. The aim of the study was to find associations between biophysical factors (absolute elevation, geographical location), forests’ historical land use (forest continuity types) and present floristic composition on the islands of Saaremaa and Muhu in western Estonia. Canonical Correspondence Analysis, Kruskal–Wallis multiple comparison of mean ranks for all groups, frequency tables with Chi-Square tests and indicator species analysis were used. The Ellenberg values and hemerophoby degrees of the indicator species in forest continuity types were compared.Natural forests are associated with the areas of greatest absolute height and hence, in conditions of post-glacial land uplift, of the greatest age, while afforested former semi-natural plant communities are associated with lower (post-glacially younger) and western areas. Semi-natural woodlands covered mainly with deciduous trees, are relatively well preserved in eastern areas. The sensitive indicators of field layer vascular plant flora are the dwarf shrubs typically found in natural forests. The abundance of species sensitive to human activities (including orchids) is highest in natural forests, but also great in semi-natural woodlands pointing to the high value of these habitats. Knowledge derived from the observed relations between different land use practices and forest vegetation can be used to more precisely determine the conservation value of stands, to forecast the course of their succession, and to choose suitable management methods to support timber production or conservation.