Management of Scots pine, the most widely distributed conifer in the world, was often based on clearfelling and replanting regimes, resulting in a rather poor biodiversity value. However, there is nowadays a general expectation to increase biodiversity by applying a more complex silviculture. Although present knowledge of genetic factors is insufficient to draw firm conclusions on the desirable level of genetic diversity, it seems unlikely that current silvicultural practices will limit genetic diversity in Scots pine Native pinewoods are rare in Europe, but have a flora and fauna of high conservation value. Therefore they must be recognized as a priority habitat under the European Commission's Habitat Directive. The high conservation value of native stands is a function of their old-growth structure that provides a rare habitat. A number of measures should be taken in all types of Scots pine forests to enhance biodiversity. Firstly, old growth habitats should be promoted. Foresters have to accept that a small percentage of the pine resource should be managed upon much longer rotations. Secondly, retention of deadwood should be encouraged. Dead and dying wood are key components of stand structure and act as key substrates for many associated species, such as microbes, invertebrates, small mammals and birds. Furthermore, a complex stand structure should be promoted at both the horizontal and the vertical scale. A small scale forestry, group regeneration systems, natural regeneration, introduction of broadleaves and stronger thinnings are strongly recommended. Availability of quite precise niches significantly increases biodiversity value. Conservation of isolated populations, found under extreme environmental conditions, is an absolute need. Populations endangered either by their small size or by environmental stresses, hybridization with other species or human interference should be primarily conserved. Forest edges support a range of taxa, and open habitats can comprise many different plant community types. A large number of organisms are directly or indirectly dependent on or favoured by fire. However, enhancing biodiversity provokes also some risks. Generally, browsing is considered as a moderate risk. Introduced species, such as aspen, act as an alternate host to the rust. Open species can present a threat to the European pine marten, dying and deadwood can provide breeding habitats for pest species (Tomicus piniperda), burning increases the risk of seedlings being attacked pine fire fungus (Rhizina undulata) and forest edges may be an attractive habitat for pest insects. An extension of existing growth models is needed to incorporate biodiversity issues in forest management planning. Distance dependent individual tree growth models should be developed. Sets of indicators for biodiversity must integrate compositional, structural and functional attributes. Attributes such as species richness, species abundance, species diversity, horizontal and vertical distribution, tree age, tree size, stand diversity, architectural complexity, genetic variants and deadwood are needed for the establishment of biodiversity indices. Assessment of functional phenomena needs the knowledge of the driving biotic environmental factors.