Candidate plant species for lignocellulosic ethanol production include species within the Poaceae, Pinaceae, and Salicaceae families. For these biofuel feedstock species, there are variable amounts of genome sequence resources available, ranging from complete genome sequences to transcriptome data sets in the form of Expressed Sequence Tags. Some biofuel feedstock species have limited sequence resources. While obtaining gene or transcript sequence is the initial goal of all genomics research, the more challenging step is to functionally annotate those sequences. Computational methods are the only cost-effective means for assigning functional annotations on a large scale. Almost all computational annotations rely in part on comparative analyses that transfer functional descriptions from previously characterized homologous genes to improve the annotation of uncharacterized sequences. For the current release of the Biofuel Feedstock Genomics Resource, we have created a comprehensive, uniform, well annotated resource for data-mining gene data for biofuel feedstock species. The predicted genes from seven sequenced plant genomes and the predicted transcriptomes from 44 biofuel feedstock-related species are annotated within the Biofuel Feedstock Genomics Resource. All sequences in the resource have been aligned to Uniref proteins, InterPro domains, and KEGG Orthologs. Orthologous gene groups have been identified to allow users to easily identify relationships between genes of interest and other sequences within the resource. Search functions allow users to find sequences based on sequence alignments, functional annotation, sequence identifiers, homology to KEGG orthologs, InterPro domain names, Gene Ontology terms and Single Nucleotide Polymorphism and Simple Sequence Repeat markers.