To identify switchgrass homologs of rice genes, known/predicted to control biomass and stress response-related traits, we screened 96,000 clones from two switchgrass bacterial artificial chromosome (BAC) libraries. Full-length sequencing of 311 BAC clones revealed sequence for ∼3.2 % (51.7 Mb) of the switchgrass genome, coding for 3948 genes. A comparison with Arabidopsis and five grass genomes revealed that switchgrass genes share the highest number of homologs with rice (95.5 %) followed by foxtail millet (91.7 %) and Sorghum (91.5 %). One hundred eighteen of the annotated genes are unique to switchgrass. Gene annotation and ontology analysis revealed 695 genes belonging to gene families targeted in the screening. These include 350 kinase, 203 glycosyltransferase (GT), 109 glycoside hydrolase (GH), and 33 ethylene responsive transcription factor (ERF) family genes. Rice homologs of 65 genes, identified here, have demonstrated roles in bioenergy-relevant traits. These include 14 GT2 family genes involved in the synthesis of cellulose and hemicelluloses. Comparative expression analysis in six switchgrass organs revealed a conserved expression pattern for three cellulose synthase (CesA1, CesA2, and CesA9) and five cellulose-synthase-like genes (CslA2, CslA11, CslC1, CslD4, and CslE6). CslF genes that encode mixed linkage glucans are expressed in wider range of tissues in switchgrass compared with rice.