A draft reference sequence for the alpine carnation Dianthus sylvestris was obtained using a combination of paired-end and mate-pair Illumina libraries implemented in the Allpath-LG assembler. The initial assembly was improved through nucleotide correction, gap filling and the assessment of misassemblies, and subsequently annotated with the support of RNA-seq data through the Maker2 pipeline. The final assembly consists of ~440 MB in ~21 K scaffolds (N50 ~61 Kb) covering 86% of Busco eukaryotic genes and ~73% of the estimated genome size (600 Mb). Structural annotation includes ~22 K predicted genes (N50 ~1.8 Kb).