Provides access to data generated from high throughput sequencing of expressed genes in the flowering plant Silene vulgaris, a widely used model in studies of ecology and evolution. In Silene vulgaris Transcriptome, assembled sequences were annotated based on homology to genes in multiple public databases. Analysis of sequence variants identified 13 432 putative single-nucleotide polymorphisms (SNPs) and 1320 simple sequence repeats (SSRs) that are candidates for microsatellite analysis. Estimates of nucleotide diversity from 1577 contigs were used to generate genome-wide distributions that revealed several outliers with high diversity. All of these resources are publicly available the Silene vulgaris Transcriptome website.