The alpine plant Arabis alpina is an emerging model in the ecological genomic field which is well-suited to identifying the genes involved in local adaptation in contrasted environmental conditions, a subject which remains poorly understood at molecular level. This paper presents the assembly of a pool of A. alpina genomic fragments using Next Generation Sequencing technologies. These contigs cover 172 Mb of the A. alpina genome (i.e. 50% of the genome) and were shown to contain sequences giving positive hits against 96% of the 458 CEGMA core genes (Core Eukaryotic Genes Mapping Approach), a set of highly conserved eukaryotic genes. Regions presenting high nucleic sequence identity with 77% of the close relative Arabidopsis thaliana's genes were found, with an unbiased distribution across the different functional categories of A. thaliana genes. This new resource was tested using a resequencing assay to identify polymorphic sites. Sixteen samples were successfully analyzed and 127,041 Single Nucleotide Polymorphisms identified. This contig dataset will contribute to improving understanding of the ecology of Arabis alpina, thus constituting an important resource for future ecological genomic studies.