Transposition of mobile elements has been implicated in genome instability, rearrangements and therefore also adaptation to changing environmental conditions. Transposons could influence gene activity directly by transposition inside or close to coding regions by their disruption or by addition of regulative sequences. Further, class I transposable elements, which are the most abundant in plant genomes, utilize a RNA intermediate in their life cycle, therefore retrotransposons could act by producing non-coding RNAs that could affect other transcripts by RNA interference. Transposition activity is suppressed by chromatin modifications, and both classes of transposons have been shown to be activated in plants under various stress conditions and developmental stages. Using a nonspecific amplification approach, we demonstrate the differential transcriptional activation of sequences with homology to transposable elements and other associated sequences in the complex genome of Scots pine (Pinus sylvestris L.) after exposure to heat stress, infestation with pine woolly aphids, and salicylic acid and abscisic acid treatment. Sequences with homology to several retrotransposon classes and families were identified, as well as several chimeric transcript types. Some of them represent chloroplast sequence insertions into the pine nuclear genome and these sequences are highly represented in EST databases of a wide range of species. In this study, we identified several retrotransposon classes and families with differing levels of similarity with known transposable elements from other plant species, and which are differentially expressed under various stress conditions in Scots pine.