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<p>Abstract</p> <p>Background:</p> <p>Analyses of complete genomes and large collections of gene transcripts have shown that most, if not all seed plants have undergone one or more genome duplications in their evolutionary past.</p> <p>Results:</p> <p>In this study, based on a large collection of EST sequences, we provide evidence that the haploid moss <it>Physcomitrella patens </it>is a paleopolyploid as well. Based on the construction of linearized phylogenetic trees we infer the genome duplication to have occurred between 30 and 60 million years ago. Gene Ontology and pathway association of the duplicated genes in <it>P. patens </it>reveal different biases of gene retention compared with seed plants.</p> <p>Conclusion:</p> <p>Metabolic genes seem to have been retained in excess following the genome duplication in <it>P. patens</it>. This might, at least partly, explain the versatility of metabolism, as described for <it>P. patens </it>and other mosses, in comparison to other land plants.</p>