Advances in whole genome sequencing have allowed identification of genes for disease susceptibility in humans. Inspired by these results, our research aim was to exploit whole genome sequences of 13 rice (Oryza sativa L.) inbred lines to identify non-synonymous SNPs (nsSNPs) and candidate genes for resistance to sheath blight, a disease of worldwide significance. Whole genome sequencing by the Illumina GA IIx platform produced an average 5X coverage with ~ 700 K variants detected per line when compared to the Nipponbare reference genome. Two filtering strategies were developed to identify nsSNPs between two groups of known resistant and susceptible lines. A total of 333 nsSNPs detected in the resistant lines were absent in the susceptible group. More than 200 genes with selected nsSNPs were assigned to 42 categories based on gene family / gene ontology. Several candidate genes belonged to families reported in previous studies, and three new QTL regions with novel candidates were also identified. A subset of 24 nsSNPs detected in 23 genes was selected for further study. Individual alleles of the 24 nsSNPs were evaluated by PCR whose presence or absence corresponded to known resistant or susceptible phenotypes of nine additional lines. Sanger sequencing confirmed presence of 12 selected nsSNPs in two lines. “Resistant” nsSNP alleles were detected in two accessions of O. nivara that suggests sources for resistance occur in additional Oryza sp. Results from this study provide a foundation for future basic and applied research of sheath blight resistance.