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<p>Abstract</p> <p>Background</p> <p>The lycophyte <it>Selaginella moellendorffii </it>is a member of one of the oldest lineages of vascular plants on Earth. Fossil records show that the lycophyte clade arose 400 million years ago, 150–200 million years earlier than angiosperms, a group of plants that includes the well-studied flowering plant <it>Arabidopsis thaliana</it>. <it>S. moellendorffii </it>has a genome size of approximately 100 Mbp, as small or smaller than that of <it>A. thaliana</it>. <it>S. moellendorffii </it>has the potential to provide significant comparative information to better understand the evolution of vascular plants.</p> <p>Results</p> <p>We sequenced 2181 Expressed Sequence Tags (ESTs) from a <it>S. moellendorffii </it>cDNA library. One thousand three hundred and one non-redundant sequences were assembled, containing 291 contigs and 1010 singletons. Approximately 75% of the ESTs matched proteins in the non-redundant protein database. Among 1301 clusters, 343 were categorized according to Gene Ontology (GO) hierarchy and were compared to the GO mapping of <it>A. thaliana </it>tentative consensus sequences. We compared <it>S. moellendorffii </it>ESTs to the <it>A. thaliana </it>and <it>Physcomitrella patens </it>EST databases, using the tBLASTX algorithm. Approximately 60% of the ESTs exhibited similarity with both <it>A. thaliana </it>and <it>P. patens </it>ESTs; whereas, 13% and 1% of the ESTs had exclusive similarity with <it>A. thaliana </it>and <it>P. patens </it>ESTs, respectively. A substantial proportion of the ESTs (26%) had no match with <it>A. thaliana </it>or <it>P. patens </it>ESTs.</p> <p>Conclusion</p> <p>We discovered 1301 putative unigenes in <it>S. moellendorffii</it>. These results give an initial insight into its transcriptome that will aid in the study of the <it>S. moellendorffii </it>genome in the near future.</p>