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Unique physiological and metabolic properties of Arctic mosses are responsible for their acclimation to the inclement polar environment. To perform transcriptome analysis of an Arctic moss species adapted to polar conditions, we constructed a complementary DNA (cDNA) library using total high-quality RNA extracted from the moss species Aulacomnium turgidum. The library consisted of 1.81 × 106 of independent clones with 97.41% of recombinants. A total of 509 cDNA clones were sequenced. After eliminating poor quality sequences, vector trimming and clustering, 360 unigenes consisting of 33 contigs and 327 singletons were identified. Basic Local Alignment Search Tool X searches generated 245 significant hits ( E value <10−5). For further Gene Ontology analysis, 158 unigenes were annotated and classified with terms for molecular function, biological process and cellular component. Among the expressed sequence tags, seven genes were selected based on their putative roles in stress response, and they showed enhanced transcripts level under various abiotic stresses such as low temperature, heat and high-salinity. Also, two rare-cold-inducible genes showed different expression patterns under low temperature and UV-B treatment, indicating their distinct roles in adaptation to Arctic environment. Although experiments have been conducted on a limited scale, this study provides useful information for better understanding the mechanism of stress acclimation of polar mosses and material basis for potential genomic modification for higher plants to increase stress tolerance. [ABSTRACT FROM AUTHOR]