Background: Freshwater duckweed, comprising the smallest, fastest growing and simplest macrophytes, have various applications in agriculture, phytoremediation and energy production. Lemna minor, the so-called common duckweed, is a model system of these aquatic plants for ecotoxicological bioassays, genetic transformation tools, and industrial applications. Given the ecotoxic relevance and high potential for biomass production, whole-genome information of this cosmopolitan duckweed is needed. Results: The 472 Mbp assembly of the L. minor genome (2n =40; estimated 481 Mbp; 98.1%) contains 22,382 protein-coding genes and 61.5% repetitive sequences. The repeat content explains 94.5 % of the genome size difference in comparison with the greater duckweed, Spirodela polyrhiza (2n = 40; 158 Mbp; 19,623 protein-coding genes; and 15.79% repetitive sequences). Comparison of proteins from other monocot plants, protein ortholog identification, OrthoMCL, suggests 1,356 duckweed specific groups (3,367 proteins, 15.0% total L. minor proteins) and 795 Lemna specific groups (2,897 proteins, 12.9% total L. minor proteins). Interestingly, proteins involved in biosynthetic processes, in response to various stimuli and hydrolase activities are enriched in the Lemna proteome in comparison with the Spirodela proteome. Conclusions: The genome sequence and annotation of L. minor protein coding genes provides new insights in biological understanding and biomass production applications of Lemna species.