Background: Larixprincipis-rupprechtiiis a softwood tree of great economical and ecological value.Yet,this species is poorly characterized at molecular level with little sequence information available in public databases, therefore hindered the application of genomics-assisted breeding approaches.Results: With the purpose of generating the first broad survey of gene sequences for L.principis-rupprechtii,normalized cDNA collections from multiple tissues and genotypes were used to sample large numbers of expressed genes and to detect simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs).We obtained over 1,300,000 sequencing reads from a 454 GS FLX Titanium pyrosequencer (mean length: 345 base pairs).De novo assembly yielded 45,884 isotigs, with 33,880 reads remaining as singletons.Based on sequence similarity with known proteins, these sequences represent approximately 26,000 unique genes (unigene) and cover a broad range of Gene Ontology categories, and 1,123 unigenes were assigned to specific metabolic pathways by the Kyoto Encyclopedia of Genes and Genomes.We located and characterized 1,473 SSRs and 16,436 SNPs as potential molecular markers in our assembled and annotated sequences.Conclusions: Our data provide the most comprehensive sequence resource and an extensive collection of potential genetic markers currently available for L.principis-rupprechtii, permitting unigene definition across a broad range of functional categories.As well as providing resources for functional genomics studies, the unigene set has permitted significant enhancement of the number of publicly-available molecular genetic markers as tools for improvement of this species.