Hemp (Cannabis sativa) is a robust fiber crop with a wide variety of industrial uses including textiles, plastics, and construction.  Recently hemp has also been proposed to be a potential feedstock for biofuel production.  Despite its many uses, very little is known about the hemp genome, and very few genome resources are available. To better understand the genome structure of hemp and characterize how it responds to environmental stimuli we have sequenced mRNAs from hemp stem using the Illumina Genome Analyzer.  Our RNA-Seq assay produced ~46 million short reads, resulting in 320,000 ESTs after de novo assembly. An exhaustive search of NCBI non-redundant protein database identified 10 plant genomes with consistently high similarity (Populus trichocarpa, Sorghum bicolor, Arabidopsis thaliana, Vitis vinifera, Oryza sativa, Ricinus communis, Physcomitrella patens, and Zea Mays).  Using these 10 genomes plus Medicago truncatula as reference genomes, we identified and annotated 13,000 hemp ESTs with 80% or more length coverage. We are currently extending our analysis in order to estimate the expression levels of the genes involved in important pathways such as cell wall biosynthesis.