Very few genomic resources are actually available for sweet cherry. Emergence and generalization of next‐generation DNA sequencing technologies that reduce cost, labor, and time, provide the opportunity to conduct large‐scale genomic projects at lower cost even for non‐model organisms like prunus avium. In order to obtain a panel of prunus avium expressed genes for functional studies and candidate gene strategy, a normalized complementary DNA library has been sequenced using high throughput 454 technology (GS FLX Titanium) yielding 1175627 reads after cleaning. Clustering and assembly generated a total of 19574 contigs and 149688 singletons. After functionnal annotation of clusters and singletons, a web portal has been created to query the prunus avium transcriptome database. This annotated transcriptome constitute a versatile resource for candidate gene selection based on functional annotation and will be used soon as a reference for short read mapping in differential expression studies by RNA‐seq.