Brown or common rust of sugarcane caused by the pathogen Puccinia melanocephala is an economically important disease in many sugarcane industries. Genetic loci for brown rust resistance have been previously identified. This study was undertaken to identify gene expression differences between a highly resistant accession of Saccharum spontanuem and a highly susceptible hybrid sugarcane clone, which are the male and female parents respectively of a wide cross mapping population. Total RNA was isolated from leaves of the hybrid sugarcane clone Green German (hybrid sugarcane clone) and IND 81-146 (S. spontaneum accession) and used to construct mRNA libraries for RNA-Seq. Libraries were constructed from 200-300 bp mRNA fragments and sequenced using Illumina chemistries on a GAIIx using single end read (76 bp). Sequences were mapped to the Sorghum bicolor reference sequence and also to a database of known plant disease resistance genes. Read mapping was used to compare identify differences in expression levels between the two genotypes. Assembled sequences were used to identify putative candidate genes involved in resistance to brown rust of sugarcane in the S. spontaneum parent.