Bulked segregant analysis (BSA) is a method for rapidly identifying molecular markers linked to any specific gene or genomic region. We combined next generation sequencing (NGS) of the transcriptome with BSA to identify resistance gene candidates as well as closely linked markers for the sunflower locus PlARG conferring resistance against Plasmopara halstedii. The transcriptome of two bulks (resistant and susceptible) was sequenced by 454 pyrosequencing, yielding a total of 428 Mb from the resistant bulk and 429 Mb from the susceptible bulk. A computational strategy was developed to mine the NGS data for marker candidates that show distinctive SNP patterns or presence-absence variation between the two bulks. In addition, we filtered for genes with homology to known resistance genes. We successfully verified candidates that are either cosegregating with or closely flanking PlARG. Our results demonstrate that the new BSTA method is a powerful approach to enrich molecular markers and to identify candidate genes in the targeted mapping interval in a large and not fully sequenced genome.