The thermophilic filamentous fungus Sporotrichum thermophile (Myceliophthora thermophila) is a proficient decomposer of cellulose, suggesting that it will be a rich source of thermostable industrial enzymes for lignocellulose degradation.  To identify the genes and proteins involved in this process, we explored the transcriptome of S. thermophile growing at 45 ºC on either glucose or barley straw by short-read sequencing of extracted mRNA.  Approximately 10 million RNA fragments from each sample were mapped to the S. thermophile genome; the number of fragments mapping within an annotated gene is a measure of that gene's expression. Of the 8276 genes with measurable expression, 738 (9%) showed evidence of differential expression and 131 had at least 85% probability of differential expression; 101 of these were upregulated on barley. Most of the upregulated genes have no annotated function; their further study should deepen our understanding of lignocellulose biodegradation and uncover novel enzymes.